I believe the problem with comparison is that depending with the light which an issue is viewed in, the opinion on the matter changes.
The difference lays in what's justifiable in the historical context and what is not.
In the time of AJ, the slaughter of millions of native occupants of North America was justifiable, since at the same time in Europe was in full colonial fledge. That doesn't make it any less brutal.

Sadly, historical processes don't happen at once for everybody and that makes an assumption like "a certain culture being a bunch of radical nuts" very thorny and extremely short sighted. After all, every single country has gone through unstable periods and others of great splendor.

Unfortunately, some countries are more prone to flaunt the reflected glory of victories from the past. Taking these great deeds and absorb them as a sort of worldly mission to eradicate the unruly is at best a crass mistake.
Despite the efforts of the Inquisition, we're not all Catholics, despite the efforts of the Nazis Jews still exist, despite the Imperial Japan's efforts China still stands... and I could go on in this list for too long than it is worth.

The States also have their share of eradication practices and radicalism, so to be so quick in classifying some as terrorists, while broadening the definition for it stems, imho, from the same tree the previous references do: "If you're different than I am and won't do as I say, I'll kick your butt".
i.e. Macarthur and the "chasing out of communism", the witch trials in Salem, slavery and on more recent events, the Chilean and Argentinian dictatorships of the 60's and 70's, the Iran Contras scandal, the Iran Irak war, Egypt, Panama... and even more sadly, this list also could go on.
The US hand in these events is less than righteous, so the ethic foundation for separating those, in the manichean sense, between the good and the evil is more than uncalled for.

Respectfully,

FS