It seems odd, because speaking as an atheist, the man's faith is utterly irrelevant to me. I don't follow sports, so the only reason I even recognize Tebow is that I live in the Denver area, and it was virtually impossible to avoid seeing stories about him in the local media. My reaction to him (other than, largely, indifference) is to wish the man the best.
The only reason to wish otherwise (as far as I can tell) is that many are, at their core, antitheists rather than atheists.
They seem to only direct their ire towards Christians, they seem to be pretty okey dokey with Muslims.