This is a big issue. I see it all the time in Christian circles and in naturalist circles. If a Christian expresses doubt about God (for instance), he is shunned and accused of not believing in God. As soon as a scientist raises doubts about evolution (for instance), the same happens to him.
I have a few things to say about this. First, for both situations, the people doing the shunning are afraid to be challenged. They are scared that if their precious ideas are questioned, then they might be found to be lacking or even false. These people tend to be committed to an idea rather than the truth. This is not good for anyone. Read my post "Why Should I Challenge My Own Views?" for more information.
I would like to say that just because someone doubts something does not mean that they disbelieve it. What this comes down to is confidence and certainty. Certainty requires that you be 100% sure of whatever belief you hold. As long as challenges are around, 100% certainty is not possible. So, we have to fall back on confidence. Based on evidence, we can hold that we are, say, 90% sure and 10% unsure. If we are 90/10, then we can confidently believe something. However, if we are 40/60 (40% sure and 60% unsure) then we cannot confidently believe it. Most Christians and scientists fall into the 90/10 category for their beliefs. If they doubt a certain piece of evidence, question a detail, or challenge the existing form of the idea, they are only changing their percentages to, say, 80/20 or 70/30, they are not likely taking it to 50/50 (agnostic- don't know) or 40/60 (disbelief).
Now, I must say that the more a view goes challenged or questioned without those challenges and questions being answered, the percentages will continue to shift until they hit that "magic" 49/51. Then the person is disbelieving, but not because they challenged or questioned, but because they were not adequately responded to.
When someone asks a tough question its because they are struggling with it, not because they are ready to "jump ship". In both the Church and the scientific community, we need to stop accusing those who are challenging us of being "traitors", and help them along. If an idea is true, then all challenges and questions to and about it have an adequate response. By ignoring those people, we only show that we don't believe that last statement ourselves.
Michael Patton from Reclaiming the Mind Ministries wrote a blog post about this same issue: Can Christians Doubt. Please read the comments (19-103, specifically). A reader challenges Michael on the biblical merits of his claim (same as mine). Michael defends his position, and with the help of another reader, the offended reader realizes they are saying the same thing, just with different nuances that took focus.
Michael recently published another article "The Sufficiency of Probability in the Christian Belief". This is another great article worth reading.
Greg Koukl of Stand to Reason is asked if one can still be a Christian, yet have some doubts. Here is his answer:
Koukl is also asked "How could struggling with doubt be good".
Here are some great Christian podcasts I have found that address the deep questions and tough challenges to its worldview (pretty much every podcast on the right side of my blog):
Stand to Reason
I Didn't Know That
Without A Doubt