I read that article a while ago and am glad you brought it up!
For me I never found BBT funny because it hit too close to home. I've studied and worked at Caltech, with many people who identify as high-functioning autists, and have a family member with AS. Unfortunately, due to my experiences, I read the some of the "geeks" on the show as crude caricatures of individuals with ASD.
Whenever I mention my experiences at Caltech, people will always stop and ask: "So was it like BBT? Was everyone nerdy, socially-awkward, and weird?" (These comments are never made in a positive light). In BBT, the characters are something to direct laughter, scorn, and incredulity at. I found it hard to watch this show with friends, listening to them berate and mock the "geeks." None of them viewed Sheldon with any sympathy... and yet when they would meet my family member they'd remark on how much they reminded them of Sheldon.
It bothers me especially because now, instead of recognising how wide and multifaceted the autism spectrum is, people are lured into the trap of prescribing preset characters to anyone they meet with ASD. "Oh, you have autism; ergo, you must be like Sheldon/Sherlock/Rain Man."
I don't fault anyone for liking the show, I'd just encourage them to me conscious of how certain characters are portrayed. But then again, I just may be too sensitised... it's hard to find something that won't rub someone the wrong way. In the same vein, I know many people who have had family member experience incarceration and cannot stand the rampant inaccuracy in Orange is the New Black.
Wow. That was rambly. Time to step away from the keyboard...