Personally, I'm willing to accept the Theory of Evolution as the most possible expllaination for the diversity of life, but that doesn't change the fact that there are a lot of flawsin that theory. Also, athiests who demand total secularism at all times are practicing their own sort of religion.
There are actually two different elements labled "Evolution". There is the "fact" of Evolution, in that we know that creatures used to be different than they are now. Then there is the "theory" of evolution that attempts to explain why these creatures evolved. There are valid disagreements in science about this, which agenda agencies like the Discovery Institute seize on and promote as "flaws" in evolution theory.
At the fringes of science there are always disagreements that can be sold as "flaws". But this is a dishonest tactic, and only done by people with an agenda other than truth.