To answer your first question, we agree with the fact that he is a Copt, although perhaps not practising, but I don't think that played into getting him arrested for what he said or wrote and then being tried militarily.
Indeed, he is not the only prisoner of conscience. There were other people arrested before he was and also after that. For example, earlier I mentioned the actor. He's not in prison because he still can appeal the decision; he's out on bail.
But that is just to say that the system is there to crush dissenting views and opinions. Without a change and without serious amendments to the penal code, Copts and Muslims—and anybody—can indeed find themselves in prison for expressing their views against human rights violations, but also for generally expressing their views about social, religious, and economic phenomena in Egypt in general.
To answer your second question about the sympathy towards Maikel Nabil, I think Maikel Nabil was sentenced very early on when a lot of people still believed that the military were indeed one hand of the people. It took a long time to demystify the simplistic view of the position of the military council. This might account for some of the lack of sympathy towards Maikel's case in the very beginning. That's my view of it.
I think Maikel has gained a lot of confidence and is coming out stronger from this case. He is currently pursuing his work to actually end forced conscription into the Egyptian army, to allow conscientious objectors not to be recruited into the army. He has come out of prison stronger than before and remains a noticeable activist in Egypt.