I watched it, thought he came off pretty good. Well spoken and some humor. I thought the comparisons to Howard Hughes were off base; there is a difference between being eccentric and being totally off one's onion!
Sometimes really driven people can't understand that not everyone is as single-minded as they. We've seen it in sports, for example, as well.
The only thing I didn't really like was Stahl referring to "search for aliens" which makes it sound like some UFO conspiracy theory. Actually the Search for Extraterrestrial Intelligence is a serious scientific project that was funded by NASA until their funds were cut. Allen stepped in and covered costs, and there are people in the scientific community who are very glad of that.
Overall he came off a lot better than Sarah Palin did, but that' setting the bar pretty low!