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He most certainly was. His whole point was based on the color of his skin.

Making a statement based on the color of one's skin does not immediately constitute racism.

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from dictionary.com:
1. The belief that race accounts for differences in human character or ability and that a particular race is superior to others.
2. Discrimination or prejudice based on race.

Limbaugh's statement was that he felt the national media was showing favoritism towards McNabb (because of his race), that he was overrated.

What exactly about his statement was "racist"?
- The media has been very desirous that a black quarterback can do well...- Rush is saying that the media is overhyping a QB (any QB) because there are not many black QBs in the NFL. That doesn't sound racist towards blacks. This could be viewed as a perosnal opinion of the media, not of McNabb.

- There's a little hope invested in McNabb, and he got a lot of credit for the performance of his team that he didn't deserve. The defense carried this team.- This sounds like it could be a simple statement of fact that could be applied to ANY QB.

Looking at the numbers in that Slate article, I'd say that it was a reasonable assessment to say that the defense was the strength of that team.
But, it has been McNabb that is able to garner the majority of the attention, right?