Previous studies of the original cast of Transformer characters have shown a few times where an Autobot character blurred the lines between "good guy" and "bad guy." This complexity was not limited to the Autobots. Thundercracker is perhaps the earliest example of a Decepticon who, although undeniably on the wrong side, is just unsure enough about why he fights on the side that he does that one can imagine possibly swaying him to come over and join the good guys.
That said, Thundercracker's never quite defected to the Autobots' side yet.
For one thing, Thundercracker has a definite superiority complex. He can fly. Most Decepticons can. Most Autobots can't. Humans certainly can't. According to Thundercracker, those who can fly are better than those who can't. For Thundercracker to become an Autobot, he'd have to come to an epiphany on the value of life that goes against some of his most fundamental beliefs.
There's also the fact that his fellow Decepticons would make life very difficult for Thundercracker (if, indeed, not outright impossible) if they suspected that he might betray them.
I've stated before that Thundercracker, along with fellow Seekers Starscream and Skywarp, was one of the very earliest "repaints" in the history of the Transformers franchise. I've managed to used toys for three different molds for each of the Seeker entries in this series of "Thunderous Thirty" posts, but it bears noting that every one of the molds used in these three entries has been used for all three characters (although the Skywarp toy using this mold may not quite be in stores yet at the time of this posting). This particular mold represents the Seeker form as it appeared in the "Fall of Cybertron" video game, thus representing a pre-Earth form, which has since been "re-adopted" by certain characters in the modern IDW G1-related comic lines. In fact, this particular Thundercracker toy comes with a pack-in comic that demonstrates his sense of uncertain loyalties rather nicely.