Everyone always thinks Logan would repress his feelings for Wade, that he would deny them to himself and anybody that implied he liked Wade as anything more than a friend, but honestly? I think that would be Wade.
Logan has never really been one to hide his emotions. He doesn't hide his attraction or affection for people. Jean is a great example. Logan knows that she and Scott are together, but he doesn't hide that he loves her. He makes it known.
Why wouldn't he with Wade? He doesn't have any competition, and finally he has a place to call home, so why would he hide his feelings? Wade flirts with him and makes jokes about being it's wife, so why would he feel the need to hide it?
Wade though? Wade is insecure, anxious and let's be real- a complete mess. He doubts peoples feelings towards him, friends or otherwise, and he pushes people away when they get too close. When he starts to realise that he loves them.
Logan has to try and break that barrier. He assumes Wade is worried about being hurt again by someone he loves, when in reality, Wade is worried about hurting Logan.
Wade knows Logan wouldn't hurt him- not unless they were fighting together in the way they both loved. He knows Logan isn't going to leave and that he loves him. Wade hates that he knows that, because Wade doesn't trust himself enough to not ruin that. To not ruin Logan.
Wade has been treated so poorly in the past- basically being blamed for everything bad that's happened to or around him- and he's begun to believe the things he's been told, the things people say about him.
Vanessa had broken up with him because he didn't prove himself worthy. He wasn't enough- so how is he meant to be enough for Logan?
Logan is confident in his feelings, Wade isn't and he never has been.