I wonder if some if it is the idea that murder is done for Reasons (whether they be good, bad or otherwise, there's usually some plot behind it) whereas rape is not usually shown as something done for specific reasons. Regina killed, hurt and kidnapped people for very specific reasons, most of them selfish and evil but all mentioned, whereas raping Graham was for no reason other than enjoying it. Same goes for Owen in Torchwood (he was my least favourite character and this was a big part of it, though Tosh mooning over him was a bigger part!)

Still, I'm trying to think of plots where rapists have a purpose for what they do, and the only two I can think of showed the (male) character as the antagonist. There was a Criminal Minds episode where a man with terminal cancer was raping women who had been to a fertility clinic in the hope that they would keep the baby and give him "immortality" that way. In the X-Files episode, the character used his shape-shifting powers to impersonate Luke Skywalker and impregnate his ex-girlfriend who was a huge Star Wars fan (plus swapping other men's sperm for his own at the fertility clinic where he worked...hmm there's a theme here!) Still, those are shows with regulars vs antagonists in most episodes, and most of the antagonists are shown as evil when they murder, too.

Oh, another one from Buffy: Faith-in-Buffy's-body and Riley! She has a reason (to take everything of Buffy's) and she is treated quite sympathetically; it's Riley who gets in trouble from Buffy for not realising. So maybe it's the lack of an in-character reason that gets people riled up?