It's okay to cry over your dad. And believe it or not, he is probably crying over you. I'm willing to wager if you give it enough time, things will work out. It did for me and my dad.
Why not make the first step towards reconciliation and send him a letter telling him what you told us? I wouldn't, however, bring up your religious differences. Concentrate instead on the interests you have in common and on all the good times you shared together. Let him know you miss him and would love to see him again.
My thoughts are with you during this difficult time.