Everyone agrees that McNabb is having a crappy season, but the Limbaugh comment is that McNabb was never very good. He was ranked 7th in QB rating last year, and has multiple pro bowl picks as well.
I think the main issue here is whether people can talk about race without being racist. So many people are afraid of the subject that they avoid it (and people that might make it come up) thereby supporting an invisible type of racism in itself. It is more healthy for Rush to voice his opinion (which does not disparage McNabb's race, but critically analyzes his abilities and the media's perception and coverage of those abilities).
McNabb's performance may be affected by the discussion, but that is always the case with sports critics. There is no racism preventing him from making the team and doing his very best. The fans don't care what color he is. They just want him to score or be sacked, depending on their allegiances.