Alyssa Rosenberg argues that Captain America: The First Avenger lacks any acknowledgement of Armed Forces segregation because The Avengers is about "institutional optimism."
I'm not buying it. Not just because these kinds of issues have been ably handled in the comics, but the most recent Avengers storylines have been conflicts about institutional corruption, from Civil War to villain Norman Osborne's brief takeover of the Marvel Universe's superpowered national security institutions. And this is in keeping with a general trend in comic books during and in the aftermath of the Bush administration, reflecting growing American distrust in government.
Nor is the film completely ignorant of its historical context with regards to prejudice. Peggy Carter, Cap's love interest, alludes to institutional sexism briefly in one of her first conversations with Steve Rogers, saying that she knows what it's like to have "doors slammed in her face." It's easy to see how a similar scene could be constructed to explain the presence of Gabe Jones in Cap's elite unit, something along the lines of Cap insisting that he be included because he knows what it's like to have "doors slammed in his face," alluding to his earlier conversation with Carter. That would be entirely in keeping with the narrative context of the movie itself, and even Cap's character, without requiring a lengthy tangent on segregation in the armed forces during World War II.
Some people reacted to my original post by pointing out that it's meant to be historical fantasy. Well, obviously, but some suspensions of disbelief are inherent in the genre: Sci-fi weapons, super-soldier serums, ect. Erasing segregation isn't. While I'm not demanding that the film be a really serious portrayal of the European theater during WWII, it's not really too much to ask that it treat the existence of black soldiers as carefully as it did Carter's presence in the film. What we decide to include or exclude from our fictional reimaginings of history says something about what we think is important, or even what we'd rather forget.