If you are playing with Revolutions, having a second holy city that is not your state religion is very very harmful. If you don't garrison that city with 10-15 troops, you're likely too lose it. Even then, you still might have to bribe it for a long time.
I have to respectfully disagree.
Playing on emperor level (I know, this is not the highest one

) typically I start with founding Zoroastrism/Judaism (for the already mentioned reasons: money makes the world go round

) and will in most cases get Hellenism, Taoism, Christianity and Islam.
Other religions are dependant on the course of the game.
You will have to be careful with your holy cities, no doubt, but the effects are within a bandwidth which you can easily control (how could I afford founding all these religions, otherwise?).
It may have something to do with the fact that I am playing on giant/gigantic maps, as these make the game feeling epic.
I don't know whether smaller maps may have a bad influence, but for me it easily works.
It is important that these cities will produce enough culture, which I feel to be even more important than the garrison, which typically consists of 5 - 6 units.
Concentrating on Stonehenge, Oracle and Petra (of which I should get at least 2), boosting their effects with priests will give you enough prophets to even bulb some religions, next to the construction of the shrines.
Of course, it is most important not to lose such cities.
The rest is fun.
