It is difficult to tell from the report if Tebow disagreed with the church's stance on controversial issues (I doubt it since the same report states that he's a member of another Southern Baptist church), or if he's just not prepared to take on the challenges that would be bound to come (as if he hasn't already had to deal with plenty).
As a defender of the truth of Christianity, this story caught my attention. I can't help but think that if Tebow's church had taught him, not only what to believe but, why he can trust that his beliefs are, in fact, true; then maybe Tebow would be as confident defending the truth of his convictions as he is playing on the football field.
Tim Tebow has an incredible platform, and he has used it as best as he knows how to make known his faith in Jesus Christ. But the time has come when a deeper understanding of why he believes what he believes may be necessary to take his witness to the next level. Tebow needs to do his research and prepare to address controversy, and there are many resources available to get him trained. I don't expect him to be some fantastic philosopher or theologian (right now, that doesn't appear to be his primary calling), he just needs to be prepared to "give a reason for the hope he has" (1 Peter 3:15) to those who will ask honestly and those who will challenge insincerely.
Like the vast majority of people, Tebow does not have the time to go extremely deep into the study of Christian apologetics. That is why many apologists have written basic-level books and provide quick and easily accessible resources that will begin the training and give them more confidence to address controversy. Two of my favorites for beginners is Lee Strobel's books and the resources as Stand to Reason. If you don't have time to read books, Bobby Conway at The One Minute Apologist has numerous short videos where leading defenders of Christianity answer common and difficult questions.
As I've mentioned many times in the past, the parts of the Body of Christ need to build each other up. Tebow may not even be aware that such resources are available to strengthen his mind and his heart. We, as defenders of Christianity, need to let him (and others in similar situations) know that we are here to support them. God has placed these people in view of the public for a reason. Let's be the support that ensures he is successful at the purpose God has place him there to accomplish.
Other resources to get you started:
Please Convince Me
The Poached Egg
Apologetics 315
Other posts of interest:
Is Faith Emotional or Logical?
Can Religion Be Tested For Truth?
The Courageous Movie and the Purpose of Apologetics