Actually, one of my favorite things about Star Trek is the lack of "villainous" villains. A lot conflict is because of cultural differences and misunderstandings rather than what things devolve to in the time of the Star Trek movies.
I partially agree.
It's true that many of Kirk's adversaries had a James Bond movie-like flair to them (Anan 7 of "A Taste of Armageddon" comes to mind) that made them stand out as simultaneously dangerous and gentlemanly.
This made them somewhat nasty, and immoral from the audience's point-of-view, but not necessarily guilty of "cruel" villainy. In a sense, Anan was standing up for the (questionable) values of the system he spent his entire life being a part of, so that confrontation was more of a cultural clash.
By contrast, Proconsul Claudius Markus ("Bread and Circuses"), who personally murdered Flight Officer William B. Harrison of the S.S. Beagle, comes across as a brutal aggressor. Yet again, Markus was also a natural product of his "Roman" culture, and simply behaved as one might expect the leader of a corrupt industrial-age empire to behave. (Putin, anyone?)
So yes, many of the adversaries Kirk encounters are just aliens trying to confront what they may see as a potential threat to their "way of life". (Krola's words in the excellent TNG "
First Contact" episode from 1991)
Still, not all of TOS' "bad guys" fall into this category. Nomad may have been a machine, but its ruthless quest to purge every world it encountered made it, in a strange TREKkian sense, the "cruelest villain".