I think it makes sense. The whole safe-sex thing was probably not the real issue to begin with. Simply, it made him realise you were serious about that guy. Maybe he was fine with sharing you sexually but not emotionally. Maybe he expected it to be sexual only, maybe he expected to be fine with the emotional aspect but actually wasn't.
But now that you know the real issues, you can work on them as you said
Best of luck and keep in touch to let us know how it goes.