Hemant Mehta aka The Friendly atheist boldly stated in a blog that “There’s no doubt Christians are threatened by atheists. We challenge their views, our demographics are growing, we just make more sense” He also goes onto say “The truth is, if Christianity did a better job of equipping children to deal with challenges to their faith, the Internet wouldn’t be a problem” 
Aside from citing a Christian on the fringes/extremes, he’s hit the nail right on the head; the church as an institution has simply failed to address the questions and issues that people have and take them seriously. It’s one of the reasons cited by atheists to Larry Taunton during his discussions with them . If you’re not getting answers from one source, you will go to another and conclude the previous side have no answers; that’s just inevitable and natural. Churches need to get more willing and better at answering the questions people bring to them, it’s as simple as that and I’ve recently sent a piece to the magazine sent to a group of local churches putting this somewhat bluntly . The internet has completely changed the landscape on how discussions are carried out and the amount of information that is available, but churches haven’t helped themselves by firing people for seemingly asking what they deem to be the wrong type of questions .
What all these churches seem to miss though, what Hemant Mehta seems to inadvertently admit and seems so obvious to me now; is that if you fully explore your faith, ask questions, challenge beliefs and get meaningful answers, there is nothing to fear from atheists let alone the internet. There are many websites dedicated to providing answers and resources for people who have questions. This is not to say that the challenges aren’t tough or that all the objections raised are nonsense; some atheists do raise some very tough valid objections, but you’re less likely to be surprised by them if you’ve already raised them yourself and/or in the process of working your way through them. Doesn’t mean you will have all the answers, but you will have built a platform to work from with the answers you have got; and “I don’t know” is a valid answer, just don’t leave it at that. It’s no different to studying for a degree or any qualification; the more you study, the more you know, the more confident you will be in putting forward a good argument for your case.
What makes a good argument though? Dr. William Lane Craig suggests that “to be a good argument, it’s not enough that an argument be sound. We also need to have some reason to think that the premises are true”. In short, you need to know why you believe what you do. If it’s just a case of “I’ve always believed” I’m not convinced that cuts it anymore but more on that later. It’s not enough to just know your own though, you need to know and understand the opposite side as Dr. Craig concludes; “You should compare the premise and its negation and believe whichever one is more plausibly true in light of the evidence. A good argument will be a sound argument whose premises are more plausible than their negations .” So beliefs being rational involves knowing the basis of your belief, the basis of the opposing viewpoint and knowing why your viewpoint is more plausible. As a Christian, I obviously believe that Christianity is more plausibly true in light of the evidence. An atheist will believe the same about atheism, David Mitchell for example, believes that about agnosticism . We all believe we are right, but being logical doesn’t automatically equate to being right. A conclusion is rational if it follows logically from the data but a conclusion that follows logically from flawed data is both rational and wrong (thank you to Sarah, Ian, Robert and Rebecca for their input on that). You can see this with science as conclusions change as more data becomes available.
As Christians we are under pressure to provide justification for why we believe what we do, but I see this as a good thing. It may cause a period of doubt and uncertainty  but Thomas went through that and at the end, was able to confidently state “my Lord, my God” The only reason Christians have to be afraid of the internet or atheists is if your response is “I believe because I always have” I suspect some atheists would have similar responses to why they’re atheists and they have every reason to be afraid too. Christianity is much more than just a set of intellectual exercises and responses, it’s about relationship so ask yourself this question about any relationship you have; why am in this relationship? Or think about why you’re not in relationship with someone and ask why. Then ask would I be with this person if I took the same stance as your faith; “just because” and you may begin to see why it doesn’t work and you why need to know why you believe.
Knowing why you believe is just as important as knowing what you believe.