Proper scientific reasoning inevitably leads to atheism because faith is absolutely epistemologically incompatible with science. That’s a fact and nobody who tells you that “science and religion are compatible because there are X number of practicing scientists who are religious” is actually addressing that – the practicing scientists in question are simply not applying scientific reasoning to their religious beliefs, that’s why they somehow manage to keep them (which also happens to mean that those are some very poor scientists who shouldn’t be calling themselves so, but that’s a different conversation).

There is nothing wrong with pointing this out. It may be a bad strategy in the short run because of flawed legislation (while it is true that it has been used to keep creationism out of schools, in reality the First Amendment is no friend to the cause, because it also prevents any serious attempt to relegate religion to its rightful place in society where it will have no influence on anything that matters; unfortunately few people realize that or dare to go there), but in the long terms it is an even worse strategy to deny it.

The problem is that many atheists use (often distorting) science as an indoctrinating tool for their atheism. Then, they are shocked when science loses support. Richard Dawkins is an example.

You see it here in Discover. For example, the (very bright) Razib Khan has an (amazing) blog about evolutionary science but he usually speaks about atheism or links one of her old entries about atheism.

This is good and dandy but it would be better for him to have a blog about atheism, instead of including his ideology in a web about science.

Then, people are amazed that science can be such a divisive issue.

Over here, evolution is just recognised fact.