This is interesting because there's a similar situation in my life but to answer your question I have to say "Yes" by all means if you and this man love each other, I say marry him!
Somewhere in the bible it states when a wife marrys her husband in that union she should be devoted to her husband first, not her father. I understand you're not married yet, but if your Dad has met him and there is something about him he doesn't like, then adhere to what your dad sees because men know other men. My dad always told me he could tell where a man is coming from by his hand shake and his conversation. So pay attention to that. But, if he's never met him and is just not ready for his daughter to marry yet then that's when you make this decision for yourself and please yourself.
Don't let your love get away behind what your Dad says because you may have regrets later about it.
A good way to test the love you have for each other is do the Pros and Cons game. It's good for both of you to play this game. Write down all the good he is to you and his qualities, then weigh those bad things that you may not like about him or the bad things he does. In all sincerity, if the good out weighs the bad then this could help with your decision.