I think the tile bonus pantheons go up and down in value (compared to, say, GotH) depending on map size. If you're playing normal or smaller, there's way too few resources of the same type around you (apart from maybe quarries or pastures) to make them worthwhile. I never tried it, but in Civ5 (and to some extent in Civ4) the map generator tends to clump up resources by type, especially on a continents script, so you'd have like an area with 10+ Sugar tiles.
Yeah, especially since the distribution of luxuries is pretty random, most of the time you'll only have at most 2 of the "related" luxuries. Plus combined with the fact that, for example, Goddess of the Hunt (+1 food per camp), food is generally of marginal value anyways, I can't say I've ever taken that.
And then you combine some pantheons that are just so brutally horrible that I can't believe they even exist (initiation rites +50 faith per camp cleared, or roughly speaking less faith from that than an average chop), and it's definitely far from balanced. My personal algorithm for pantheons is basically:
1. If running a religious game with a large stretch of tundra/desert, take that pantheon
2. Goddess of the Harvest
3. If running a coastal game, Goddess of the Sea
4. Earth Goddess
5. If going for early military, God of the Forge
6. Divine Spark
7. If I do have a cluster of cows or banana, the culture pantheon
8. City Patron Goddess
Outside of those 8 choices (10 pantheon options), I think the only time I've deviated from those have been as the Khmer I've chosen River Goddess since that meshes perfectly with their ability. I've been tempted once or twice by Stone Circles, but you need an almost perfect terrain for that to even make sense. As far as I'm concerned, you could take any pantheon other than those listed, double its output, and I don't even know if it would make my list except in the most extreme of cases.
I'll also take this as a small chance to rant that they failed to add some new awesome pantheon choices with the expansion. Especially with the disasters, there was a golden opportunity to add something volcano related, or like a "God of Destruction" pantheon that would like reverse the effects of blizzards and tornadoes. Can you imagine some sort of pantheon like "any unit of yours damaged in a natural disaster gains a free promotion"? That would be such a crazy pantheon to play with, that would be totally awesome figuring out how to exploit it.