"Starting from the position that the government is lying to you is just as stupid as assuming they're always telling the truth."
If this is true, then the rational position would be to assume that the government may or may not be lying to you. Which is what I believe.
"'The government' is hardly a single entity."
The people are different, but if the Milgram experiments (and sociology in general) have taught us anything, it's that a person's social influences are as important to their decision making as their intrinsic character. And the laws, rewards, and punishments are largely the same across departments.
I realize the EPA is different from the FDA. However, the reasons why the EPA buried studies about the amount of mercury in freshwater the day before issuing new guidelines on acceptable mercury levels are largely the same as the reasons why the FDA approved OTC plan-B only for women 18+.
The takeaway is that bad things don't (usually) happen because of bad people. They happen because organizational behavior, psychology, and sociology allow us to make an educated guess that if an organization looks like X, then what tends to happen will be Y.
Now if I see patterns across organizations that you don't see, maybe that makes me a conspiracy theorist and maybe I'm seeing patterns that aren't there. Or maybe I just see patterns that you don't see.
I agree that at the end of the day you have to think about these problems individually for yourself. I don't actually believe the vaccines are all that dangerous, but at the same time I'm not going to take them just because the CDC or NIH or whatever say they are safe. The reason is that the people running these departments are operating under largely the same structures and incentives as the people running every other government department, and history as a whole shows that these sets of structures and incentives tend to produce unsavory behavior.