There are groups that provide assistance and support to LGBT teens who are struggling social ostracization, coming out, or escaping an abusive home life. There are not nearly enough of them, but at least the need for this sort of support is widely recognized. This is not yet the case for atheist teens. Perhaps the plight of Damon Fowler will lead to some progress in this area, as more of us realize what some atheist youth must endure.
An example of how this is already beginning to happen can be found in the form of Atheist Havens on Reddit. The idea is simple: compile a list of people all over the country, who are willing to take in atheist youth who have been thrown out of their homes due to their atheism. While such a system is fraught with legal difficulties given that we are talking about children who are likely to be un-emancipated minors, it is a start.
I believe that another important unmet need involves figuring out effective mechanisms for providing support to atheist teens who have not yet been thrown out of their parents' homes. Obviously, there is a great atheist presence here on the Internet. That is certainly better than nothing, but it would be nice to supplement it with telephone hotlines and local support groups.
I have written about the need for local atheist support groups before. I think this could be extremely helpful, especially in communities where there were no visible atheist organizations. For those of us interested in seeing an increasingly secular world, finding ways to support atheist youth should be high on the list of priorities.