The fact that many of the Kriegsmarine might not have been Nazi party members themselves is well documented, but signing up to join a military force, this is the sort of chance you take. I daresay there are quite a few Democrats in the US Army right now who don't necessarily agree with G W Bush's policies, but follow their orders nonetheless, that they do so doesn't make them Republicans. I know many friends of mine in the British forces wouldn't p*ss on Tony Blair if he was on fire, but they still do as they are ordered, as that was the pledge they took when they signed up.
Here's some interesting takes on the matter:
Adolf Hitler: "I have a reactionary army, a National Socialist air force, and a Christian navy.'
Ace U-Boat commander Reinhard Suhren (U-564), once famously shouted up to the quayside as his U-Boat came in from patrol: 'Are the Nazis still in charge?'
Upon receiving the reply that they were, he promptly put his U-Boat engines into reverse and backed away from the dock as a joke. Not everyone was amused onshore, but the vast majority were it seems, as he never got into trouble for doing this.
U-802 commander, Helmut Schmoeckel was in fact half-Jewish, and amongst other things, he is famous for writing the book 'Menschlichkeit im Seekrieg' (ISBN 978-3813202250), which is about instances of U-Boat crews rendering assistance to allied sailors.
Many noted Allied leaders came forward at the end of the Second World War to speak up for Kriegsmarine officers and men who were under the threat of being charged with war cimes, in fact, Admiral Karl Donitz himself was not prosecuted because of testimonials from many Allied commanders who stepped up in defence of him. The same cannot be said for the Luftwaffe's Herman Goering.
And there are many more tales of a similar nature which prove the point.
U-Boat crews were noted for many transgressions from official Nazi doctrine: They regularly wore clothing other than their official issue, quite often they wore British Battledress outfits that had been captured when the Allies evacuated Dunkirk. A notion which hardly sits with the common movie misconception that U-Boat commanders spent all their time Goose-stepping up and down the interior of their U-Boat in an SS uniform.
Whilst other military units and civilians in Nazi Germany were prohibited from listening to Allied radio broadcasts (and faced stern punishment if caught doing so, men of the Kriegsmarine made no secret of the fact that they did so, under the pretence that it offered intelligence on Allied shipping.
Similarly, jazz records - another severely frowned upon vice in Nazi Germany owing to the fact that most of the decent jazz artists were black - were known to be favourites amongst the U-Boat crews. All this is also far cry from the oft-portrayed Nazi fanatic U-Boat commanders of many Allied propaganda movies, and of course, the preposterous movie, U-571. The portrayal of this in Das Boot might be seen as somewhat apologist to many, but it is apparently very close to the truth, although Karl-Friedrich Merten refuted some of (the book) Das Boot's portrayals in his own book 'Wir U-Bootfahrer sagen: "Nein! So war das nicht!' (We U-Boat men say: No, it wasn't so!).
So if it really bothers anyone to simulate driving a U-Boat around, they can take solace from this if they choose, but at the end of the day, it's a computer game, and I'm pretty sure playing it won't turn you into a Nazi.
Anyway, Sieg Hei... ooops, I mean, erm, have fun.
Chock