Aren't all the robots supposed to be BLU? (Despite the fact that Valve decided to just make it just RED defending agaisnt BLU robots instead of the trailer which was RED + BLU agaisnt gray robots but it isn't very surprising as Valve take every chance they get to favour RED and beat up BLU.)
I think they chose to make it red versus blue just to make gameplay easier. I have trouble enough shooting at the wrong team in regular multiplayer maps anyways, so adding another color to the mix would just make things worse. The players are wearing red, meanwhile, because it's a defense situation against attacking robots, and RED always plays defense.
My personal favorite in-story explanation for why it's all RED versus blue robots is that the BLU team is borrowing RED uniforms to keep the RED sentries from targeting them. It just makes too much sense.