There is a rumor, to put it nicely, going around right now that the designer of the second flag of the Confederacy was a man named William T. Thompson. Thompson was clearly a racist and wrote of fighting to “maintain the Heaven-ordained supremacy of the white man over the inferior or colored race.” Yuck.
This seems to have originated on the Twitter account of Jonathan Wilson, who apparently holds a PhD in US History from Syracuse University. I would have expected someone with a PhD in history to actually pay attention to the context surrounding one smaller excerpt, but apparently reading comprehension isn’t as fun. Now all of these different websites, mainly news sources, have copied the information and treated it like gospel. Then of course there are all the memes floating around featuring the same information. Which would be all well and good if it were completely accurate, but as usual it is a grain of truth with more omitted.
Mr. Wilson lists this as his source, a book entitled History of the Flag of the United States of America which was published in 1880 and available as a free ebook on Google Books. In it is excerpts from editorials written in the Savannah News by Thompson, including the above terrible quote.  However, if you read it you also find that Thompson was not a part of the committee which designed the flags and seal, the House, or the Senate. He was not even in the same city as those making these decisions, and had to receive news of the approved flags via dispatch. While we are told by this book that they approved a flag like what Thompson wrote of and had been submitted a design by him, it is clear they were considering a great number of design options and trying different options with modifying them.
The flag approved by the Senate was not in actuality what he had suggested, but rather a field of white with a blue stripe which makes sense since the Confederacy drew inspiration for their flag from the Scottish flag, the St. Andrew’s Cross, which is blue and white, and they were trying to move away from the appearance of the United States flag. The House decided they didn’t like the appearance of the blue stripe so removed it, and the flag as it was made was of different dimensions than what Thompson had talked about due to inconsistencies with the revisions between the Senate and House. Revisions that were done without Thompson being anywhere around.
George Preble, author of the above book, also wrote one entitled Our Flag: Origin and Progress of the Flag of the United States of America which had been published earlier. This book gives similar information, but more regarding the timeline of the flag’s approval. Thompson’s editorial with the very racist comments was published after the Senate had already approved the flag with the blue stripe, so Thompson’s design had to have been either nearly identical to designs that were already being looked at or it was his design but he revealed his own thoughts on the symbolism after the fact. There were two propositions for changes, either removing the blue stripe entirely or instead of a blue stripe making it a “broad blue border.”
On May 20th, 1863, a correspondent wrote to Thompson at the Savannah News, saying “Mr. Editor, you are one of the admirers of the new flag” and proceeding to inform him of the difference in dimensions which had been “established by law.” This being information also listed in the same books, only a couple pages past the excerpts Wilson chose to quote. I don’t know about you, but typically I don’t refer to the “designer” of something as an “admirer” of it. This quote tells me that there were people in the Confederacy, if not the majority of the Confederacy, that never would have considered Thompson the “designer” of the second national flag despite his having submitted a design and commented on the process.
Additionally, all of this regarding the second national flag occurred after the Confederate battle flag, the flag currently being debated in the media, was already designed and in use. THAT FLAG most certainly had nothing to do with Thompson whatsoever.
So then, what? Are we supposed to be shocked there were racists in 1863? This should surprise no one. There were racists everywhere! Thompson himself wasn’t even from the south originally, but was born and raised in Ravenna, Ohio. However, to take a newspaper editor’s opinions and say they represent what the Confederate House and Senate had in mind for the symbolism in their approval is quite a leap, and for this to continue spreading is an example of horrible journalism.
It’s similar to how the South Carolina’s declaration of causes for secession cited hostility regarding slavery being of importance, Virginia chose to merely point out they had a right to secede and planned to do so, Texas cited the Federal government’s failure to offer any protection of Texan lives against Native American tribes or Mexican bandits, and Georgia mentioned slavery but also went in depth regarding how the Federal government was deliberately subsidizing industry of only the middle and northern states while allowing the south to pay taxes for it:
“The material prosperity of the North was greatly dependent on the Federal Government; that of the South not at all. In the first years of the Republic the navigating, commercial, and manufacturing interests of the North began to seek profit and aggrandizement at the expense of the agricultural interests. Even the owners of fishing smacks sought and obtained bounties for pursuing their own business (which yet continue), and $500,000 is now paid them annually out of the Treasury. The navigating interests begged for protection against foreign shipbuilders and against competition in the coasting trade.
Congress granted both requests, and by prohibitory acts gave an absolute monopoly of this business to each of their interests, which they enjoy without diminution to this day. Not content with these great and unjust advantages, they have sought to throw the legitimate burden of their business as much as possible upon the public; they have succeeded in throwing the cost of light-houses, buoys, and the maintenance of their seamen upon the Treasury, and the Government now pays above $2,000,000 annually for the support of these objects. Theses interests, in connection with the commercial and manufacturing classes, have also succeeded, by means of subventions to mail steamers and the reduction in postage, in relieving their business from the payment of about $7,000,000 annually, throwing it upon the public Treasury under the name of postal deficiency.
The manufacturing interests entered into the same struggle early, and has clamored steadily for Government bounties and special favors. This interest was confined mainly to the Eastern and Middle non-slave-holding States. Wielding these great States it held great power and influence, and its demands were in full proportion to its power. The manufacturers and miners wisely based their demands upon special facts and reasons rather than upon general principles, and thereby mollified much of the opposition of the opposing interest. They pleaded in their favor the infancy of their business in this country, the scarcity of labor and capital, the hostile legislation of other countries toward them, the great necessity of their fabrics in the time of war, and the necessity of high duties to pay the debt incurred in our war for independence. These reasons prevailed, and they received for many years enormous bounties by the general acquiescence of the whole country.
But when these reasons ceased they were no less clamorous for Government protection, but their clamors were less heeded– the country had put the principle of protection upon trial and condemned it. After having enjoyed protection to the extent of from 15 to 200 per cent. upon their entire business for above thirty years, the act of 1846 was passed. It avoided sudden change, but the principle was settled, and free trade, low duties, and economy in public expenditures was the verdict of the American people. The South and the Northwestern States sustained this policy. There was but small hope of its reversal; upon the direct issue, none at all.” 
The opponents of the Confederacy and of the Confederate flag seek to make this a far simpler and clearer cut period of history than it actually was. They depend on the Union having a moral superiority so that they can point fingers and condemn those who wish to remember their Southern heritage. It is not that simple though, and never has been.
 In the referenced books the newspaper was referred to as the “Savannah News,” but other sources refer to Thompson’s paper as the “Daily Morning News” or the “Savannah Morning News.” These all refer to the same publication.