Unfortunately, this show was a particularly intelligent one for people who AREN'T particularly religious (or are filled with doubt, or have problems with the classic view of God).
It had issues with appealing to actually highly religious people. I won't detail them much, but the one PC sop, having God appear as a rather effete male, suggesting that it's ok to be gay is sure to annoy some religious types, with adequate Biblical argument on their side (regardless of if oyu agree, it's still going to annoy many highly religious people). I think it should have been either left as a topic-to-be-avoided (such as denominational issues, including judaism, Xtianity, and Islam) or confronted head on, with some sort of acknowledgement of what the Bible states but leaving the fact that it's between each person and God rather than something to be enforced by others. The show did neither, which did not help.
That said, there was a movement by some Xtian groups to write-in to save the show, so not all Xtians were sufficiently offended by the show, which was on the cusp after the second season. Its initial popularity obviously surprised the hell out of CBS -- there's a reason they put it in the Friday Night Death Zone in the first place (remember, The Passion of the Christ came out in 2004, the first Narnia in 2005. Joan debuted in 2003).
Another issue -- God is not supposed to appear to anyone again, after Jesus, until the Second Coming -- i.e., there are no further prophets (including Mohammed) -- which I have no problem with in the context of the show, as it is certainly never claimed or suggested that Joan is a prophet -- but I know at least one person who cited the Biblical passage as an excuse to reject the show unseen, and yes, I think he's an idiot. So its basis can chase away part of the "obvious" audience, Xtians, while not making its appeal known to the actual target -- people open to belief but who have problems with the classic view of God. This show is very good for people who consider themselves Agnostic or even somewhat Athiestic, or who have Really Serious Doubts -- because I believe it presents a view of God which is more humanistic and rationalistic than many "official" views. If the basis for your disbelief and doubt is associated with problems with the "classic view" of God, this show may provide you with a view you will find more acceptable to your own sense of Right And Wrong. I think that God, in this show, makes sense in light of the problems in this world. That can be a basis for Faith.
I'm not making any promises -- YMMV -- but I think it's a fantastic show, exceedingly well written, with excellent acting and characters, and it does address issues with God, and The Problems of the World (and why God may choose to not interfere) with a remarkable level of intelligence and wisdom. If you don't believe in God, you may, watching this show, find a view of God which you can respect and believe in.
At the very least, the show can be a good source of some great late-night BS sessions in a college dorm about religion and its place in society. And that's not necessarily a bad way to find religion, either.
It is unfortunate that the show ended so abruptly, but, despite the cliffhanger series end, it's still very much worth the time spent watching it.