Indeed, those who most loudly attempt to ridicule and discredit conspiracy theories tend to focus on defending against criticism involving the powerful.
This may be partly due to psychology: it is scary for people to admit that those who are supposed to be their "leaders" protecting them may in fact be human beings with complicated motives who may not always have their best interests in mind. And see this.
For example, Obama's current head of the Office of Information and Regulatory Affairs - and a favored pick for the Supreme Court (Cass Sunstein) - previously:
Defined a conspiracy theory as "an effort to explain some event or practice by reference to the machinations of powerful people, who have also managed to conceal their role."
He has called for the use of state power to crush conspiracy allegations of state wrongdoing. See this, this and this.
Michael Kelly, a Washington Post journalist and neoconservative critic of anti-war movements on both the left and right, coined the term "fusion paranoia" to refer to a political convergence of left-wing and right-wing activists around anti-war issues and civil liberties, which he claimed were motivated by a shared belief in conspiracism or anti-government views.
In other words, prominent neocon writer Kelly believes that everyone who is not a booster for government power and war is a crazy conspiracy theorist.
Similarly, psychologists who serve the government eagerly label anyone "taking a cynical stance toward politics, mistrusting authority, endorsing democratic practices, ... and displaying an inquisitive, imaginative outlook" as crazy conspiracy theorists.
This is not really new. In Stalinist Russia, anyone who criticized the government was labeled crazy, and many were sent to insane asylums.
Using the Power of the State to Crush Criticism of the Government
The bottom line is that the power of the state is used to crush criticism of major government policies and actions (or failures to act) and high-level government officials.
Pay attention, and you'll notice that criticism of "conspiracy theories" is usually aimed at attempting to protect the state and key government players. The power of the state is seldom used to crush conspiracy theories regarding people who are not powerful . . . at least to the extent that they are not important to the government.