I'm thankful for your concern for your son's spiritual life, because the most important legacy we can ever pass on to our children is our love for God. Even if they choose to turn from it for a time, they will never forget that God was real to us, and our lives were centered in Him.
What your son is going through is common–but that doesn't make it any less serious. Perhaps he's away from home for the first time in his life, and the temptation is strong to spread his wings (so to speak) and assert his independence. He also may be surrounded at college by people who think religion is only for uneducated people (which isn't true), or are infected with intellectual pride. They also may reject God because they want to live without any moral restraints.
What should you do? First, pray for your son, that he will realize his own need of God and make his own personal commitment to Christ. Then let him know that you love him, and that you always will love him–just as God does.
Avoid arguing with him, however; as the Bible says, "A gentle answer turns away wrath, but a harsh word stirs up anger" (Proverbs 15:1). Instead, tell him that even if you can't answer all his questions, others do have answers–if he's willing to find them. Your local Christian bookstore can help you with this.