My problems with lens flare and shaky cam are that it screams camera.
Now that seems odd to say. We're watching something that was filmed on a camera. Right?
Well that's my point, I don't need to be reminded of that. Unless it's excessive, it usually isn't a bother for me (STID, I didn't notice it, ST09 was right at the edge of bugging me). If the script, acting, and all the other pieces work, I can get over poor stylistic choices most times.
Maybe cause I've watched to many straight-to-video, shot on video, B-movies, but excessive shaky cam and over the type "realism" stands out worse with digital video filmed shows and movies than it does on those shot on filmstock.