"Tolerance" isn't really a useful concept here--it is something that really only exists in dichotomy with intolerance. In order to tolerate someone you need to believe they are wrong in a significant way, but be willing to overlook that. For example, I do not "tolerate" people who think coffee ice cream is superior to chocolate chip cookie dough because I don't find our differences significant enough to merit the concept.

Likewise with Roman religion, universal orthodoxy was simply unimportant. It might be important for people in Rome to carry out rituals in the correct way, but it was unimportant that people in Britain did them in a different way. There was a general acceptance and understanding that different communities did things in different ways.

These cults, however, were threatening because their specific practices threatened the social order. Bacchanalia, for example, fundamentally shattered crucial distinctions of class and gender. Druids were often loci of provincial revolt, and supposedly engaged in practices like human sacrifice. So Roman religion did not condemn differences in general, merely particular differences.

I read an interesting article the other week on this kind of issue. 'The Organization of Roman Religious Beliefs' by Charles King, published in 'Classical Antiquity' 22 2:275-312.

Like what Tiako said, tolerance and intolerance weren't Roman concepts. Christianity, and for that matter Judaism and Islam, are concerned with 'orthodoxy', which is the correctness of belief. To be a Christian, you HAVE to believe that 'Jesus is Lord'; this defines membership to the religion. Roman Paganism was NOT concerned with orthopraxies. You inevitably had to believe that the gods exist, and that they hear your prayers, they want sacrifices, and can affect changes. But you do not HAVE to believe the 'Jupiter is Lord' - you can believe that 'Amun is Lord' and still be a Roman Pagan.

Building upon this, Roman Pagan gods had ASPECTS - for example, Mars was the god of war, but he could also be invoked to protect someone's fields, because he had multiple aspects: one for influencing battle, one for influencing harvests. Another example, Catullus writes about the goddess Diana, saying that she is

"called Juno Lucina by those suffering the pains of childbirth. You are called powerful Trivia and Luna with the counterfeit light... May you be hallowed by whatever name pleases you..".

You can see here that the goddess Diana, in different forms, had different names and different areas of control. Thus when Roman Pagans encountered other gods and deities and systems of worship, they could choose to believe that these new gods are other aspects of their gods. Thus Amun, the lord of Egyptians, could be conceptualised simply as a different aspect to Jupiter, lord of the Romans. Furthermore, if one person wished to invoke Mars to protect their fields and another invoked Dionysus, and a third invoked the lares, none of these people would conflict with each other; they respected their choices and had their own respected in turn. This answers why certain religions were accepted and not persecuted.

As for the other part of the question, it relates to ORTHOPRAXY, which is the control of acts and rituals. This was the domain of the Roman Pagan priesthood; it was their job to ensure religious rituals were carried out in the proper manner. What the Bacchic Cult and Christianity did is meet outside the established orthopraxies. Christianity had its own leaders, it unified and equaled the classes, and refused to acknowledge the established Roman Pagan hierarchy and obey its commands that they sacrifice in community with the rest of the Empire. Hence the persecution of Christians.