Horray, I get to be outraged about something! Outrage is what us Trek fans live for!
But seriously, he probably posted the letter he got from you on his blog to amuse his friends.
Yeah, this is one of those people who can't tell the difference between a well written show that is not the sort he enjoys and a badly written show.
Star Trek is certainly not beyond criticism, it's got a lot of flaws in a lot of places. But he didn't address any of the legitimate criticisms of the series, he just kind of went on about pajamas. And he singles it out among shows like Hannah Montana without mentioning things like Jersey Shore, The Real World, Jerry Springer, Whitney (Or any of the mostly cringeworthy three camera sitcoms out there), any Seth MacFaralane show, any of the one season CSI clones they've tried. His mention of Star Trek clearly has more to do with a particular axe he has to grind rather than making a thoughtful list of cringe-worthy shows.
And with South Park he mentioned it has "Some great episodes and some cringe-worthy episodes". I agree with that completely, but if that is a case you're counting, no mention of Saturday Night Live? It's had entire cringe-worthy seasons, and it's run sketches weekly for years that weren't funny the first time!