It details the mechanics of the system established at the end of the Time of Troubles, in which a divine figure's relative power would be determined by the quantity of their worshipers.
Faiths and Pantheons also features the power levels and exact abilities of the various major deities of Faerûn (those with divine rank 15+), as of 3rd Edition, and has descriptions of the dogmas and churches of all of the intermediate deities, lesser deities, and demigods named in the setting's core rulebook. It even features the names of various monster deities and others unmentioned in the core book, with descriptions of some, as well as 20 prestige classes for player characters and non-player characters alike.
Erik Mona commented on the book's design: "The new design ethic was to focus on building the Realms into an interesting campaign setting for players and DMs, above and beyond an adherence to old material so far out of date a modern-day graduate student could have been in grade school when it first went out of print. So I did my best to infuse deities like Deneir, Selune, and even poor little Cyrrollalee with interesting, occasionally challenging ideas that they hadn't been exposed to in the long history of the Realms. When ground has been covered eleven times before, it's really tempting to just parrot older material, changing the exact wording but not worrying too much about updating the gears that make that material work. For Faiths and Pantheons, I tried to tear some of these gods (particularly some of the lamer ones) to their core concepts and build up from there. That's not to say they're so different as to be unrecognizable--they're the same deities, but some of them have new, hopefully interesting aspects to their characters and motivations that haven't been revealed until now."