The Marvel we know and love of today was created by Stan Lee. Lee, himself grew up Jewish. As his life progressed, though, Lee doubted these beliefs in part and became an agnostic. Personally, he knew what he believed, most of which was of Christian ways, but couldn't quite fit them into any certain doctrine. Intentionally or not, this style of thinking became his style of writing.
 
Even without regard to Lee's personal beliefs, we can still find a logical explanation within the pages of the comics themselves. In the Ghost Rider comics, we find areas where Satan (later renamed Mephisto) has come for Ghost Rider's soul. However, he is stopped by none other than "The Friend", a character which is basically Jesus in human form. Other times, we see characters described as the supreme or one above all. Arguably, The Living Tribunal, Eternity, and Infinity could possibly be characterizations of God, Jesus, and the Holy Ghost. 

Now I know that many of you are thinking "Excuse me. What about Thor?" and I get that. The thing with Thor, Odin, and the like is that they aren't really 'gods'. They are actually described as aliens from another planet. Hence, Asgard was able to be placed floating over Oklahoma during the Siege story arch, because, if it were a divine place like Heaven, it would not be visitable by mortals. This is also how Marvel includes Namor of Atlantean legend, Hercules of Greek mythology, and Ares in the comics alongside Asgardians. Throughout the comics, Marvel has tended to stick to the common belief held by most mainstream characters: "There is no such thing as magic; it is just science that hasn't been discovered yet." Most prominently, Doctor Strange's abilities have been described as 'enhanced cellular repurposing'. Wanda Maximoff, the Scarlet Witch, basically only has the mutant ability to alter probability. All of these give the illusion of magic but in essence, aren't truly magic.

All in all, Marvel DOES have a basic or theme religion: Christianity with a teeny dose of Secular Humanism. Then again, what does it matter? Does anyone actually read comics for spiritual guidance? No. Of course, not. That's why we have Bibles. :)