and tolerance of the intolerant was never a theme.

I'm sorry but this is bullshit. I cite episode 1-2, season 1. Q places Picard and the Enterprise on trial for the misdeeds of the human race. This character and plot re-emerges many times throughout this show and others. As recently as Picard season 3. Q's accusation is that the human race is guilty of crimes. He calls humanity a "dangerous, savage child-race." He's right, of course, which is what gives the theme gravitas. Picard's ongoing game with Q is a form of atonement rather than a test. The theme is that us humans are clearly fallible, and guilty of much, but also capable of heroism and feats of bravery and altruism.

Star Trek isn't Star Wars, with a baddie and a goodie. The three shows I cited explore the grey area between what you think is right, and what someone else thinks is right. They are powerful and thought-provoking precisely because they don't treat the audience like children, or parishioners in their pews. "Tolerance of intolerance" was one of the central themes in Star Trek, because the writers demanded we explore the nature of our morality ourselves. As a Star Trek fan I'm surprised to be explaining this to you.