Yes, there are more dimensions to politics than 'left' and 'right', but it does indeed seem that the security services are always worried about a certain type.
And then you have the IRS specifically targeting right wing non-profits.
The tax categorization these organizations were applying for is meant to exclude political activism, so flagging organizations with explicitly political names was a reasonable approach.
Actual militia groups.. I mean, Oklahoma City happened, right? Imagine if there was a group of hippies or, god forbid, Muslims with the level of rhetoric that some of these militia groups have along with the training routines and arsenals to prove they're serious.
My beef with how the police treat hippies and muslims is the well-documented, "infiltrate, keep suggesting violent actions until someone says 'maybe', then arrest them" routine. If someone's suggesting violent actions ahead of time and making actual preparations for such without prompting, then that may actually be a threat. Regardless of politics.
EDIT: This is not to say the ATF acted appropriately at Ruby Ridge or Waco. They shouldn't be the first ones shooting.
Whereas COINTELPRO on the other hand...
Libertarians are theoretically on the sidelines of that debate if not fully on the multiculturalist side. I guess discussions like this one separate the actual libertarians from the crypto-republicans.
The Tea Party generally gets permits for its rallies, and complies with insurance and crowd control requirements. Occupy and WTO protestors generally do not. This is sufficient to explain all or most of the differences in treatment.
His book on the subject ("The Authoritarians") is incredible, and has a lot to say about the rise in authoritarianism that has been slowly creeping into today's politics.