The real issue about Rand Paul’s religion is not what he believed in college, it’s what he believes today. Paul says he is a Christian but at the same time he also says he is a disciple of Ayn Rand.
Sorry, but that’s pure crap. You can’t be both at the same time. Just take a look at what Ayn Rand said about religion:
Ayn Rand on God:

Every argument for God and every attribute ascribed to Him rests on a false metaphysical premise. None can survive for a moment on a correct metaphysics.

Ayn Rand on Faith:

…. The alleged short-cut to knowledge, which is faith, is only a short-circuit destroying the mind
Faith is the worst curse of mankind, as the exact antithesis and enemy of thought.

Ayn Rand on Christian Compassion:

Now there is one word–a single word–which can blast the morality of altruism out of existence and which it cannot withstand–the word: “Why?” Why must man live for the sake of others? Why must he be a sacrificial animal? Why is that the good? There is no earthly reason for it–and, ladies and gentlemen, in the whole history of philosophy no earthly reason has ever been given.
It is only mysticism that can permit moralists to get away with it. It was mysticism, the unearthly, the supernatural, the irrational that has always been called upon to justify it… one just takes it on faith.

Mysticism, of course, was one of Ayn Rand’s favorite synonyms for religion and her view gets genuinely vile when you add in her countless statements that literally dripped with contempt and loathing for the weak, the helpless, the needy – the people Jesus called “the least of these”. Her “Virtue of Selfishness” described such people as contemptible failures and parasites — inferiors to be despised, not comforted.
So here are three questions the press should demand Paul answer:

1. You have described yourself as a follower of the libertarian philosophy of Ayn Rand but Rand was a militant atheist who said that every single argument for God is false. Which view do you reject today — Ayn Rand’s “objectivist” philosophy or Christian belief.
2. Ayn Rand said that faith is a “curse of mankind”, one that “destroys the mind” – how can you call yourself a follower of Rand and a Christian at the same time?
3. Christianity is based on compassion; Ayn Rand’s doctrine of “The VIrtue of Selfishness” says Christian compassion is not just wrong but contemptible. Which of these two doctrines do you disavow?

It’s possible that at this late stage of the campaign Rand Paul might just throw Ayn Rand under a bus to win the election (it would certainly be consistent with her advice to be totally selfish). But he’s already shown various times that he absolutely hates to disavow his extremist libertarian philosophy. As a result, questions that force him to directly face a choice between the doctrines of compassionate Christianity and Ayn Rand’s genuinely vile philosophy could produce some interesting fireworks.
Update: as the exchange in the comments section indicates, Paul could try to avoid the challenge posed by the questions above by quibbling about whether or not he is exactly a “follower” of Ayn Rand. A questioner need only replace the word “follower” with “stong admirer” to prevent this attempted evasion.