It seems with all the evil acts he has done in his entire adult life.
From murdering and restoring Bor only to have him killed.
Or having Asgard be brought to it knees by Osborn and his cronies.
Or during Defalco run where Loki killed or was it seriously injured a friend of Thor and numerous other examples.
I know that they're brothers (Or is it THEIR? I think that it's they're.), but still. Come on. There (That one I know to be right. Thank you very much.) are brothers that don't talk to each other, and family members that avoid one another. Or don't really love (Or even like.) each other. Or hold grudges. After everything that Loki has done, relations or not, Thor shouldn't be THAT sad to want him back. Fraction was asked about this and said that Thor was thinking "Logic of the heart" or something similar to that, but I still can't bring myself to buy it. Logic trumps emotion. At least it SHOULD. Not that emotion can't play a big factor into things (Especially things related to family.), but for Thor, this is a big DUH moment.