Like Aquaman said, nuclear subs (well, probably all of them, but I'm not sure if there are any diesel boats in the Navy anymore) are designed to penetrate the Arctic ice cap so the conning towers are quite strong. Plus, as is also mentioned, these boats are designed for combat, ie., they are not only armored to withstand extreme pressures from just travelling at extreme depths, they are also armored to resist explosive detonations from enemy munitions.
Fishing boats are designed with waves in mind. BIG difference.
The thing that floors me about this whole incident is how unlikely it was. Think about how big the ocean is and how relatively small these two vessels are. I suspect that the statistical chances for this occurring are nil. The civilian at the helm was NOT the cause of the accident since it isn't like they leave them at the controls without supervision. Also, it's likely, though I haven't any experience on a sub, that the helm is rather useless during an emergency rise to the surface, which they were practicing (they blew their tanks to rise quickly). It's not like they were gradually coming to the surface on a slow glide.
As I see it, the captain made two mistakes. He strayed beyond the designated sub training area (which is common, but probably should be avoided) and then when he did decide to do a practice run of a rapid resurfacing, he didn't make DAMN sure there were no ships around since he was outside of that training area. He was negligent in that regard, and the civilians had nothing to do with that. The media just likes to drum up stuff to make the military look bad.