They were only aligned with us after we overthrew their democratic secular government in 1953, and installed an unpopular authoritarian monarchy as sole leader. The reason we overthrew their government is because they felt we were ripping them off in oil deals and wanted the right to audit and cancel those deals (and renationalize their oil fields) if we weren't playing fair. Then in 1979 that puppet government was overthrown in a "real" revolution, which gave birth to the Islamic Republic of Iran which, for some reason, always had a chip on its shoulder against the West.

The protests in Iran today are almost certainly being extensively backed by the CIA and other US organizations. Do not mistake a minority as necessarily representing much more than themselves. Of course they might (I certainly don't have any particular insight in the "real" Iran), but you could certainly see something similar happening in the US with extreme groups, left or right wing, becoming visibly active if they were able to find a strong backing/organizing power that made them believe that they could genuinely overthrow the government. The point being that the actions and claims of those groups would not necessarily represent the US at large.