Am I thick?? 
Well, there are quite a few aspects to this you seem to have either dismissed or not considered.
Ennis' problems, like most intractible problems that can cripple a person's life, cannot be overcome just by "striving" and trying hard. This is a person who has spent his life cut off from connections to other people one way or another. Yes, he does deny himself happiness but to simply dismiss that as being 'a goof' is equivalent to saying that someone who has a problem with stuttering is lazy and doesn't care about communicating clearly because "after all, all he has to do is stop stuttering."
Here's a few other things that you might consider taking into account:
Guilt. This is a person first of all ridden with guilt over parts of himself that he can't accept, and typically people who don't feel they deserve something - or someone - often seem to throw it away. The fact that Alma Junior iis disappointed but doesn't give up trying to reach him suggests that at some level she understands that this isn't a personal rejection of her as his daughter.
Difficulty in communicating. As much as he loves his daughters, Ennis is never quite at ease around them once they're past early childhood.
A fractured life. His fears and inability to accept his own sexual nature has led him to keep his relationship with Jack his life's great secret, even as that relationship is the most important thing in his life. And it's one thing to go off on "fishing trips" when their mother is at home with them or when he's living alone; quite another, and a complication, with one or both of the children living with him.
Legal and visitation problems. This is arguably the 500-pound gorilla in the room. Ennis might not be well educated but it's amazing how quickly people can get an education about family law when they get divorced; especially when children are involved.
At this point in the story, Alma clearly knows what his relationship to Jack is, and an attempt to get primary physical custody, which is what Junior is talking about in the legal sense, would involve a court hearing and a family law judge going over every detail he/she can get hands on. Ennis' financial situation would be contrasted to Alma's and Monroe's and Alma might just see this as the final straw that would get her to go public about the reason their marriage broke up. If she should do that, Ennis would not only
not get custody of either of the girls, he might well lose visitation rights. If he'd had a heterosexual affair, that revelation in court might not be as traumatic for him but the result would likely be the same and this is still true in family law in many states.
Sometimes a cigar is just a cigar. The reasons Ennis gives Junior might not be the whole story, but they're legitimate reasons. Ranch work isn't a Monday-Friday 8:30-5:00 deal; it involves very long hours and frequent absences. Again, do-able when he was married and their mother lived in the same household; not necessarily a good living situation for a teenage girl at this point. And he's probably aware that her complaint about Alma and Monroe "being too strict" with her is to some extent a teenager's perspective and necessarily limited.
Maybe not the complete answer and it doesn't let him off the hook entirely; but 'trying harder' simply can't address every human tragedy or smooth over every rough spot in family relationships.
