I'm glad you have so much confidence in the government, regardless of which administration is in power. And that they don't cover up for each other.
Any of the basic assumptions underlying the grand conspiracy theory - Yousef was working for the AQ/Saddam joint venture; This JV blew up Flight 800; This JV blew up OK City - is HELPFUL to the positions of the Admin. For what purpose do you presume they would bury these things?
It comes down to the difference between snippets and proof. There may be snippets that can be interpreted in a certain way. One can presume that the lack of anything more, in words or actions, from the government means that the snippets are just that, and don't pan out as proof under the microscope. This doesn't prevent people from pointing to the snippets and trying to connect dots without any proof of the line between the dots. The other possible presumption is that the snippets are indicative of a greater truth, which bolsters the fundamental case presented by the Admin for its actions, but which is buried by that same Admin for reasons unstated.
Occam says the former is more likely.