Hell, the Troubling Doctrine

I’m a Christian, but not cut to the traditional Catholic or Protestant cloth, but part of a much smaller group of people of who differ in some crucial ways from some “traditional” Christian doctrine. In particular, I sympathise with people who are troubled by the the ancient doctrine of hell. Specifically, the doctrine of hell defined as the eternal, conscious punishment of the wicked (refer to Wikipedia article for an overview of Christian hell doctrine). Over the years I’ve heard a number of atheists challenge the goodness of God over the hell doctrine. But, is the problem with the message that we can find in the Bible, or is the problem with the message that has traditionally been given by the churches?