I think that it is a little strong to say that organized religion was their greatest enemy, but it is certainly true that they thought it was a hindrance to human society.
The reason for this was that the philosophes put their faith in rationality. They thought that the way to solve the problems of humanity was to attack them with reason. Through reason, solutions could be found that would create a better society. Because religion is not based on reason and rationality, the philosophes disliked it. They felt that organized churches were likely to stand in the way of rational reforms because the churches were wedded to an irrational and, to them, superstitious belief system.