Bayle's philosophy was based on a profound skepticism about human knowledge, derived originally from his admiration of the ancient Pyrrhonists but applied strictly to the new science and philosophy of his own time. Locke's Dutch friend Pierre Bayle stirred controversy by reviving interest in Pyrrhonian skepticism among French and British philosophers.

Bayle, like a modern day Pyrrho, uncovered serious problems in modern philosophy. He attacked Cartesian rationalism, claiming that our limited faculties gives us little reason for confidence in divine veracity. Next, he claimed that the fact that animals reason casts doubt upon the dualistic account of human nature, with its emphasis on our immaterial souls. If animals are all matter, and they think, then why can we not say the same of man?

Pyrrho next turned his attention on the empiricists. Bayle stated that Locke's careful distinction between primary and secondary qualities could nott be defended, since instances of perceptual illusion arise with respect to both. We thusly have no reliable information about qualities of either sort. Therefore, the use of representationalism in defence of scientific knowledge inevitably drives us even further into skepticism.

While I'm sure it's just a coincidence, Bayle, who was a protestant, felt that religion and morality could be secured even in the face of such skepticism, because they depend in no way on the achievements of reason. (I would agree that religion is unreasonable) Moral conduct, like all human behavior, results (in theist and atheist alike) from the irrational influence of emotion, desire, and shame (Here he may be pointing to hedonistic drives.) True religion can be based only on an entirely unreasoned faith.

Bayle was not a cold fish when it came to religion, however. He delighted in pointing out contradictions between theological tenets and the self-evident dictates of reason, and in this he was as perceptive as any non-theist.

In doing so, he takes on a philosophicl enemy of mine: Saint Augustine. He does much to "destroy this wretched Apology of St. Augustine" in his work Philosophical Commentary on the words of the Gospel, 'Compel them to come in' . Read it to see how a man can be both a thinker and a christian.

However, since Bayle held that reason was the weak sister of irrational modes of knoweldge, he used the fundamental irrationality of Christianity, such as seen in the work of Augustine, to support a rigorous fideism about god and revelation. In other words, since christianity was illogical and irrational, he held it to be more likely to be true.

Sources:

Pierre Bayle, Historical and Critical Dictionary: Selections, ed. by Richard H. Popkin and Craig Bush (Hackett, 1991)
Pierre Bayle, Political Writings (Cambridge, 2000)