At Slate, David Auerbach summarizes philosopher Rebecca Goldstein’s take on why Socrates died:
Goldstein [in her new book, Plato at the Googleplex] argues that Socrates was ultimately executed because he deferred to no one’s authority and tore down Athens’ idealized image of itself. In the claustrophobic public life of Athens, Socrates was tolerated (barely) when times were good, but condemned as a dangerous nuisance when things took a turn for the worse. When Leslie Gelb, reflecting on the rush to war in Iraq, spoke of the media and foreign policy experts’ “disposition and incentives to support wars to retain political and professional credibility,” he explained exactly why Socrates (who, like Plato, never took payment from students) was so irritating to the chattering classes of Athens: He ruined their credibility. His message, paraphrased by Goldstein as “Don’t be so hasty in donning yourselves with laurels,” fits America all too well today.
In other words, substituting status markers and authority for critical thinking is how most people roll, and woe to anyone who says, especially with good reason, “The emperor has no clothes.” It punctures the bubble of rectitude. It brings mystification before the bar of scrutiny–which, of course, it can rarely withstand.
So Socrates was brought to trial for the same reason Dostoevsky’s Jesus is brought before the Grand Inquisitor in The Brothers Karamazov: question miracle, mystery, and authority and you get hated.