They are entirely secular. They don't receive their powers from a specific deity unless that is the fluff you choose to use, unless the fluff description has changed in the transition from 3.0 to 3.5 (As far as I can tell it hasn't).
As far as I can see a Paladin is a Roland, Galahad or Lancelot (now there's a fallen Paladin). They are the best of secular Knighthood (or whatever warrior class) and they often become Clerics, but they certainly don't have to be ordained. Joan of Arc is probably another example. They are certainly pious, but they don't have to be members of the clergy.