The Chicago Manual of Style "lowercases such pronouns, but it’s not wrong to uppercase, especially if you are writing for a religious readership or anyone else who might take lowercasing as a sign of disrespect. In matters of style, in contrast to those of grammar, there are few right or wrong answers. Different houses follow different style guides in order to make their publications consistent." **
But some Bibles don't even do it, so why should I?
That said, I'm no grammar*** nazi. So as long as you can spell and don't double space your sentences, I won't yell at you if you slip up on the proper capitalization of monotheistic deity references.
* This particular debate is now happening in the comments here.
** The AP Style Guide also uses lowercase pronouns to refer to God, and "'hell' is not capitalized, but 'Hades' is [and] 'Holy Spirit' and 'Holy Ghost' are both capitalized...[as is] 'Satan'...but not 'the devil.'" I think "God the Father" should also be capitalized - but not necessarily every reference to God as the "father" or "son" should be capitalized.
*** Technically, capitalization isn't really the same as grammar or punctuation as much as it's own separate thing.