It's easy to confuse actors with scientists these days.
Nye has done much work in the field, and has a legitimate claim to be a defender of science.
Unfortunately, in this particular debate, with this particular venue and audience, he did not come properly prepared, and did not present the strongest arguments for them.
Here's the deal: people like Ham and his audience don't care about the specifics of science, evolution or origins.
What they want to know is: how much of science must they reject in order to hold onto their traditional religious beliefs?
Ham went a long way towards reassuring them that they need only reject "historical science" (which allegedly "can't be proved") while they can freely study and work on all other "observational science" without violating any fundamental understandings of scripture.
By stark contrast, scientific-Nye addressed none of their real concerns, and instead on occasion found those "deeply disturbing".
Nye's arguments were addressed to a much more average American audience & students, and as such he found little sympathy amongst Ken Ham's Answers in Genesis followers.