What decides what we trust?

It seems that with regard to a lot of things we can't trust certain sources, but is it really necessary in some cases? It's understandable with some things, like with 9/11 topics and government statements or similar, but its it really necessary? What need do some sources have to lie to us?

Why do some feel it not a good idea to trust anyone with a .gov web address? I can't really see what the USGS for example can hide. You get a bigger than Magnitude 5 or so quake, someones going to feel it, similarly with pretty much anything natural. And why would they hide it if something was up with Yellowstone (for example) anyway? Plenty of people would notice, think how many people visit or work there. Obvious activity would be impossible to cover up.

On a similar note, why does no one consider that other sources can have agendas too? I notice it particularly in 9/11 discussion, people will point out certain things, but will act as though other sources are completely right with almost fanatical devotion. How do they know that for example killtown doesn't have his own agenda to (for example) divert people from some issues.