Because they are not just mortal brothers, they are gods. And sadly, their values/ titles / realms of power are at almost perfect opposite.
Thor is the thunder god of war, warrior protector of asgard and midgard. While Loki is the god of mischief and evil. They were already meant to be that before they were even born, and have been so in many previous lives, they never got a say in it.
That doesn't mean they don't have a family bond, and don't care for each other. But fates always pit them together and neither can't help being what they are meant to be.
Loki will always betray asgard for a trick or another, and Thor will always stand up for Asgard even if Loki is right somewhere. I think that goes a long way to damage their relationship, but their more simple bond as brothers is what keep them together, despite their long and complicated history.I think it's also that Thor is not a pure asgardian, he is half earth elder god and has passed a lot of times embracing human values so he will never be as black or white as Odin when it comes to judging his brother. He knows and has often chastised Odin for being a cold, heartless father when defending Loki.
In the end, I think it's just that he loves his brother and like others in this thread have said, Thor ultimately always believes in his brother's redemption and that's why he will always forgive him at the slightest sight of repentance.On the other hand, you could argue Odin is also right and that Thor "could never stand the quiet" (when he resuscitates Loki after Ragnarok) , meaning Thor by default is a warrior protector and where does that leave him if his biggest challenge is gone.
They really are in a ying&yang relationship. Thor and Loki, minus the actual brotherhood, are essentially's Marvel's Batman & Joker.
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