From the very first episode of Smallville it is made evident that the Kryptonite meteor shower had immediate as well as delayed affects on a lot of biological matter, especially people. It is somewhat implied that exposure to the rock not only serves as a catalyst for (possibly latent) metahuman abilities, creating the early "Kryptonite freak of the week" format... but it is also implied that exposure can create a mental imbalance, as most humans that develop some Kryptonite-based ability also seem to go bad, seeking to do harm more than anything else.
Now, a lot of that could be put down to the mistreatment they suffered prior to their specific accident, or how others related to them afterwards... but it's odd that the majority of the infected fell to villainy. In that same pilot episode, we saw Lex wandering in a field during the impact, and the result was that he lost his hair. Considering again the high ratio of people who "went bad" after their incidents, though, it leads me to wonder...
Is Lex perhaps "meteor infected" at some low level, and that's why (besides comic history) he ended up turning into a bad guy in the series?
Granted, he doesn't have any powers (unless you count his survivability; dude went through more in that series than anybody else besides Clark, and still came out whole!) and yes, Lex's mindset could be easily placed on the emotional manipulations of his father Lionel... but it's also true that he was physically affected by the meteors (hence the baldness).
And, to be fair, while Lex was insatiably curious and somewhat cutthroat in business, he was genuinely protective of Clark, his family and his friends for at least the first 4 seasons. Even in a later season where he is shot and in a coma, his mind constructed a scenario where he had a positive and warm (if financially strapped) life where he married Lana and he, Clark and Chloe were close friends. And of course, there was an episode where Black Kryptonite separated his good and evil sides into two different people. Lex himself acknowledges he has a constant mental struggle to maintain his decency, saying to Clark how his friendship helps him be a better person. You can see it here, from season 4:
Granted, the writing in the series was usually top notch, blending the human drama very well with the sci-fi elements. So this could have been nothing more than playing to that drama. However, read differently ... this could be Lex admitting he has a literal internal struggle based around his personality being turned by increasing darkness he has no control over (i.e. sanity slippage due to the meteor infection.) Granted a "Villainous Luthor" is canon in most Superman media, and from childhood Lex was surrounded by less than stellar influences...but it's never been full established what mental effects Kryptonite could have on normal humans.
However, we do have evidence of Kryptonite exposure on Lex in another version of Superman causing some form of sanity slippage, as seen in Superman & Batman: Public Enemies a few years later. Granted, Lex was deliberately shooting it into his system, but the basis is still the same, as seen here:
Could it be that, in the Smallville universe at least, Lex was actually a pretty decent person, or at least had the capacity to be... but his exposure to the meteor rocks slowly made him go more and more insane, thus facilitating his villainous turn in later years?
Plot convenience aside, such an infection would also explain his high survivability throughout the series, the loss of hair, and the gradual change in his mental state, despite other occasions showing him to be a reasonable person.
