What is the best way for parents to prepare their children for the attacks on their faith they may face in college?
There is no formulaic answer and no guarantee. For a start, our children themselves are extraordinarily diverse. Many will be tempted by postmodern assumptions. Others will feel far greater threats from biologists, cosmologists, or psychologists who operate under the assumptions of raw atheism or, worse, functional atheism. All I can do is enumerate some values and practices in the home that seem to me to be wise, biblically faithful, and useful in mitigating the dangers. These are exemplary, not exhaustive.
First, the home should encourage vigorous Christian understanding. The most dangerous seedbed for intellectual rebellion is a home where faith is sentimental and even anti-intellectual, and where opponents are painted as ignorant knaves, because eventually our children discover that there are some really nice people who are atheists and agnostics, and they can present arguments in sophisticated, gentle, and persuasive fashion.
Similarly, the local church with young people who are heading off to college should be doing what it can to prepare them—first with a solid grasp of Christian essentials, and second with the rudiments of responsible apologetics.
At the same time, both the home and the church should be living out a Christian faith that is more than intellectually rigorous. It should be striving for biblically-faithful authenticity across the board: genuine love for God and neighbor, living with eternity in view, quickness to confess sin and seek reconciliation, a concern for the lost and the broken, faithfulness in praise and intercessory prayer, a transparent delight in holiness, and a contagious joy in God. Even if our children are sucked into intellectual nihilism for a while, over the long haul it is important that they remember what biblically-faithful Christianity looks like in the home and in the church.
Fourth, wisdom in shaping our kids demands more structure when they are young; more discussion, carefully monitored controls, and a safety net as they grow older; and a willingness, in most instances, to wait to be asked for advice when they have genuinely left the nest and are no longer dependent on our roof or our wallets.
Finally, pray for them. Pray for them especially diligently when you recognize, as you repeatedly will, that unless the Lord builds the house, those who labor do so in vain.