Think about it.
It seems that almost every time we see "him" appear in a story he is being woken up by cultists to cause havoc on the face of the planet. We hear that in his house at R'lyeh he waits in perpetual slumber...maybe he's just trying to get a decent nap and keep getting woken up by pesky little humans (and other lesser beings). How do you appear when you first wake up in the morning? half-asleep fumbling around to hit the snooze button? What about being woken up in the middle of the night by kids/pets/the-idiot-next-door? I'm sure that's not conducive to rational thought either.
Even in the blasphemous texts describing the monstrous old ones, Cthulhu is described as being in an eternal state of half slumber, dead to our universe until he is awoken by certain arcane rituals. I'd be half asleep too if I had people waking me up every couple of minutes (and from the perspective of an immortal being, I'd imagine a decade would probably feel like a couple of minutes). I'd be tired and irritable, and would probably go to sleep fitfully until the next inevitable wake up call.
Cthulhu might not be a malevolent being naturally, maybe it's the constant pestering by cultists that makes him that way. Maybe if we let Cthulhu have a few hundred aspirin, and a good millennium of sleep, he might wake up in a much better mood.