I should have been clearer: I think religion and science are based on different views of the world as well, and so in that sense I think they are in conflict too.
However, the "Conflict Thesis" as it is talked about in the discipline of history, has a more specific meaning: it refers to the idea that when you look throughout history, religion has always (or almost always) been in direct opposition to science and has tried to sabotage its progress for as long as it could. This is still quite popular in the public consciousness with phrases like "The Church burned lots of scientists in the Middle Ages" and the anecdotes of Galileo and Copernicus.
That's the historical version of the conflict thesis that historical scholars have pretty much unanimously abandoned. The relationship has been a complex one, and certainly not one of constant conflict: often science and a rational view of the world was supported (and in fact argued for) by the Church.
So when I say that the Conflict Thesis has been abandoned, I don't mean the idea that science and religion are not in what you might call a metaphysical conflict, but rather to the idea that they have always been hostile towards each other over the course of human history.
That's what I meant.