I think it might be because sometimes he's just mean to her. I've played her in four games...I think..and I've never played her with Rhys. I never got the Tosh/Owen shippers but Owen/Gwen. I'm all over it. I agree totally, I don't exactly think that Ianto/Jack is quite as ONE TRUE LOVE as the fandom thinks. It's hardly her fault that she's so made of awesome.
They really need to think of the icon makers when they're trying to be all atmospheric and cool. Seriously!