I'm sure things will work out fine, OP. YANBU on one hand - your husband's reasons were ridiculous. I don't pretend to understand the complexity of his relationship with his gps but that was a weird moment to pick to identify with their Protestant background (he couldn't have just taken a quick trip over to NI on the 12th, waved a few flags, marched up and down and went home with a hangover?)
On the other hand, I agree with the other posters saying YABU for not objecting more strongly at the time. If he is the man you say he is, you'd like to think that if you'd pointed out how distasteful and anachronistic the reasoning for his veto was, he'd have realised he was being a plonker and wised up.
By the way phequer you are very much sectarian.
Not sending your children to a school with a religious ethos because you're an atheist, fine. Not sending your children to a school with a Catholic religious ethos because of your Protestant non-religious heritage and the fact your dad wouldn't like it, not fine. He wouldn't like it because of his (and by extension, yours) bias against Catholics. This is bigotry. If you think it isn't, you're suffering from a fairly large plank in your eye.
My sister was born and raised as RC in West Belfast and still practices as RC. She married an agnostic Protestant. Her children were baptised as Catholic but don't practice. They both attended a secondary school with a Protestant ethos because guess what? It was the nearest school, it had really good results, it was the best choice for the kids. She didn't give a flying f**k what my highly Catholic parents thought, and quite rightly so (tbh they didn't have any issues with it - they might well have in the seventies or eighties, but thankfully have evolved with the times).
The best education, and the right choice of pastoral care/environment for the children should be prioritised over pointless and deeply rooted prejudice. Can't really believe this is even a discussion.
And I'm an ex-Northern Irish ex-convent school girl from the Falls FFS. I'd send my kids to a 'Protestant' school in a heartbeat if I thought it was a better school and environment than others.