There's a big difference between what was written then and what is going on now. Now that those people are in a position of power, they have to answer to the American people. Back then, they were just part of a think tank, writing papers that would hopefully influence others. Now they're the decision-makers. Regardless of how conservative their views are, they are held accountable for their policies, and mainstream America (and indeed, the rest of the world) wouldn't support a policy of an American takeover of the Middle East. Even if these people have those ideas in their head, they're clearly not going to execute them knowing the country won't support them.

Really, this document was just an appeal for more defense spending. Let's not get carried away here.