See, this is exactly what I was worried about. Now I've got to write a whole fucking essay because history classes never get past WWII.

"Relatively recent" here means "in the past few decades". There was a period of time in the early 20th century where (due to a long domestic propaganda effort that, frankly, you're going to have to read up on yourself) the racist connotations were significantly diminished.

During this time period, the Confederate naval jack was more broadly seen as a symbol of Southern pride. Perhaps the best example is the Dukes of Hazzard, although this was closer to the tail end of this period.

What precipitated the gradual shift to the modern interpretation was the Vietnam war. The army was racially integrated by that time, and black soldiers were encountering the Confederate flag that their Southern, white comrades sometimes brought along. For fucking obvious reasons, the "it's not racist" argument didn't exactly fly with them. To almost criminally abridge an interesting and important part of history, a symbol that those soldiers may not have ever seen or even really cared in civilian life was at the forefront of their minds.

It took years for that bad experience to move the needle of public opinion. To (again) abridge decades decades of history, that experience in Vietnam "trickled down" to the public. Over time, the mainstream view of the flag shifted from one of primarily Southern pride to one that was primarily (and later, overtly) about racism.