The stories are well-written and fun to read. You can tell that Gryphon and his friends enjoyed writing them, and they wrote them primarily for their own satisfaction, not the wide reader market.
It's only when you sit down and think about it, you realize how... formulaic they are. The cool toys. The pop-culture references. The obscure references to their friends. The angsty character flaws.
When you're MSTing, you notice these things. So, obviously, you latch on to those and make fun of them.
MSTing has never, in my not really humble opinion, ever been about punishing or flaming an author. You're not meting out justice. You're not putting the author in his place. I have never in my life seen a fanfic that has ever evoked any desire to MST in order to torment the author.
I have seen fics that have evoked a desire to MST because it'd be funny. I've seen, and MSTed, fairly normal fics that were pretty good, not at all really flawed. MSTing them were pretty funny. In fact, I prefer regular, moderately well-written fics that open themselves to some pretty intriguing riffs, rather than rampantly misspelled lemon-fests. The original MST3K riffed those bad movies because it would be fun, not because they felt the movies 'deserved' it. This is something many would-be MSTers would do well to remember.
So... yeah. Flame war? No. I can see some authors take offense at their fics being hung out for public ridicule, but many approve of it. Thinker and Ratliff have become famous, or at least infamous, from their fics being MSTed. Oscar would never have been so known. Many authors I've met are glad to have their works MSTed.
I MST for the entertainment value. I do not MST for flames. How you do it is, of course, your concern.