In early episodes that I saw, Sheldon was clueless about people and would be clumsy. He would say something about how it made more sense for him to do something because he was smarter than everyone and you felt like he wasn't trying to be mean or arrogant, he was just pointing out an objective fact without stopping to think people might be offended. That was something I could relate to and find funny.
But before too long they just made him mean. In that episode with Summer Glau, when Penny crushes his Japanese puzzle box you feel like he deserves it. He's no longer a sympathetic character whose weaknesses make him endearing. Instead he's a geek that people can feel good about disliking. Instead of giving people reason to reconsider their awful treatment of geeky peers, the show affirms that treatment as being deserved.
In real life I've met very few geeks who were genuinely mean. Most seem to believe in fair play, following the rules, good citizenship, do unto others.., etc.. However at first glance their poor social skills can make them seem uncaring.
The early episodes seemed to get that. They portrayed what geeks see in themselves and in each other.
But soon the show appealed to a wider audience by portraying geeks as non-geeks see them. Clueless Sheldon became arrogant cutthroat spiteful Sheldon. He was no longer rude do to thoughtlessness but instead became a scheming villain
People don't like geeks and this show affirms their feelings.