Accidentally helped create his son's Arch-nemises!!!

[superdoomsday]

In this situation it is not Jonathan's fault. He has every right to not trust Lex. The blame of Lex going over to the Dark Side is on Lionel, for being a terrible Father, on Clark, for lying to Lex and jumping to conclusions and lastly on Lex, just for being evil even in the first season, he smashed the guy who was giving him a parking ticket's car just because he can.

[laurarawlins]

My thoughts on this

In a way Jonathan kinda did accidentally help create his adoptive son's arch nemesis if not a major or minor way of motivating someone to turn to the dark side. Jonathan did make a deal with Lionel in order to legally adopt Clark and in exchange he sold out the Ross family business to Lionel in order for Lionel to get a foot hold in Smallville. This however had nothing to do with Lex since the deal between Jonathan and Lionel was made before lex ever became an adult. Lex was still a child at the time when the deal was made. But Jonathan's guilt on his part of the deal to sell out the Ross family business to Lionel in order to adopt Clark legally, had somehow gave Jonathan a very judgmental, a very prejudiced and a very narrow-minded outlook and perspective on rich people and therefore confused money with inner values and for this reason. Jonathan did not see Lex as his own person separate from Lionel, he saw Lex as an extension of Lionel because he is Lionel Luthor's son who shared the same last name as Lionel and he couldn't see past their last name. And found it easier to blame Lex for his father's actions and to take out his resentment and hatred for Lionel out on Lex as a way to vent his anger, guilt and regret on his part of the deal with Lionel in a very self destructive way. He could have at least channeled all that guilt, regret and anger into his farm hold chores than to projected onto Lex. Apparently Jonathan wants nothing to do with Lex and assumed the worse of him without knowing him fully. And being misinterpreted, misread and assumed the worse of can impact a person in a very emotional way. Passing on judgment onto someone else's child because you're angry and resentful of the parent of asking you for a small favor in order to legalize an adoption for you and being responsible for your part of the deal because you wanted to legally adopt a child makes no sense and is very unnecessary since the child of that parent has nothing to do with that deal that you made with that parent. IMPHO (In my personal honest opinion)

Even though Jonathan got mad at Lex for hitting his adoptive son with his car and investigating the meteors, I mean judging him solely based on his father Lionel is not enough to go off from, there's must be something more than just only Lionel to be judging Lex that harshly, all that Lex ever tried to do is help and Jonathan wouldn't let him. Like Clark said "Lex isn't perfect, Dad, I know that. But slamming the door in his face over and over only helps turn him into exactly what you think he already is."

As for Clark lying to Lex. Well, Lex did his fair share of lying to Clark as well just as much. So the whole secrets and lies thing went both ways, that was not one sided. So all the lying wasn't entirely all on Clark, Lex had a hand in that too with his lies. So both Clark and Lex both lied, but their lies was for different reasons.