Supposedly, the Ebola virus is not airborne, so re-circulated air would not by itself be dangerous. Nonetheless, I wouldn't want to share a lavatory or a middle seat with anyone suspected of harboring such a virus.
A recent caveat--there was talk that maybe this latest strain DID mutate into an airborne virus. THAT would be scary.
I've read that Ebola can be transmitted via air, although you would be in danger only in very close proximity. On an aircraft, the recirculated air is clean. Only half is recirculated, and is done through HEPA filters that remove bacteria, fungi and viruses.