Whether you are confused or missing companionship is difficult for anyone to answer because nobody knows you better than yourself.
However it seems an odd situation and reason for her to break up with you. The whole Christian thing seems like something that would be taken into consideration by someone who cared about it at the VERY start of a relationship - not 3 years into one. I've not been here long, but a recurring theme in answers to problems seems to be to "try talking to her" and i think you should stick to that standard advice in this situation.
If you decide that she is important enough to you that you want to try your best to make it work then talk to her, ask her whether that was the real reason you broke up etc.
A 3 year relationship (with no major blips besides the ending?) is one worth fighting for in my books so what have you got to lose.
Whatever you decide to do, or have done, good luck.
And in the end, the love you take,
Is equal to the love you make.
-Lennon and McCartney