The intolerance argument is a stupid one. When one person's freedom is defined by the right to limit the freedom of others, the whole system breaks down.
But for the kind of people who make the argument, nothing makes sense. Freedom of religion means freedom of Christianity. The first clause of the 2nd Amendment doesn't exist. The Bible should be on every teacher's desk, but a book with one minor gay character has no business in the library. The rights of a blob of cells outweighs those of the woman carrying it. There's not much meat on the bone.