I think most people in the submarine community attribute and suggest that ill feelings toward ensign non-quals (nubs) is based on their inability to pull their own weight. Unfortunately I don't believe that is the root cause. Think about it, as an officer, sure you may not be qualified to do a whole lot, or stand certain watches, but those are primarily OFFICER duties and have little to no impact on ENLISTED QOL. I do agree it could be part of what leads to the acceptance of treating anyone not qualified as less of an individual (especially if you realized the things they did or did not allow a non-qual to do (such as eat dessert or face the tv while eating food on the mess decks), however, in my humble opinion, it comes down to a completely different atmosphere on a submarine that does not exist on surface ships or in the Marine Corps.
First off, the many enlisted Marines I have talked to, as well as the Marine Officers and Senior Enlisted I have met, have had by far the most strict views of appropriate interactions between juniors and seniors, as well as officers an enlisted. Such as being chastised as an E-6 for not giving the appropriate greeting of the day to an E-7 while using the head...
Secondly, I would say this is to a lesser extent true from the surface enlisted and officers I have met (even the different attitudes between surface Nuke and sub Nuke).
Thirdly, sub guys are required to have higher asvab scores and consist of a crew that is made up with about 1/4-1/3 enlisted nuclear submariners) where many of them are actually smarter than the average officer and have either already completed a degree or are in the process of completing one.
Fourthly, the chiefs quarters (goat locker) is by far, way different than other communities I have come across. Firstly, they eat in the same mess deck as the rest of the enlisted. Secondly, they stand the same watches as E-6's and sometimes E-5's. Also, the head "chief"/CMC is usually junior in time and rank compared to the head "nuclear chief" where the CMC (COB) is typically a senior chief and the EDMC is either a senior chief, but more frequently, a master chief. This in some ways downplays the importance of rank.
Fifthly, the enlisted nukes went through a similar training process as the officers as well as they worked and qualified together at the same prototype. Additionally, the prototype's are for the most part, reactors that are in no way shape or form similar to the reactors on the current submarines, since most of them are from decommissioned boats/ship.
Then you have to realize that they put the brand new ensign in charge of a division in engineering, with the guys that primarily have a degree or are at least smart enough to have a degree, and their initial watches that they stand are in the "box" with the more seasoned and senior enlisted nukes on the boat. Within 2 years they are no longer in the box and no longer in charge of a nuclear division, so you rinse and repeat this interaction of giving the junior most guy to the guys who see bars as the only difference between them and it starts to create an idea that an Ensign is not REALLY an officer, just as a non-qualified enlisted person is not REALLY a person.
Lastly, and maybe the most important. They stand watch in the box, as described, where the culture is "watch team backup" which really means, if anyone screws up, you all are getting punished. This coupled with how we are required to "strongly recommend" actions, especially if they are counter to what the officer tells you, and especially considering the gravity of the situation in front of you, most nuclear operators do not trust their junior officers who are put in charge of them. It is not that we do not like them / respect them / etc, it is that they do not have as much experience, and their actions have grave consequences that puts the entire watch team at the risk of going to captains mast. I acknowledge that this scenario is similar and probably worse in many other communities, however, coupled with the other reasons above (specifically the third, fourth, and fifth) this is just my belief of why there exists inappropriate interactions of chiefs and senior enlisted with junior officers, specifically non-qualified ones.
I do not condone these views and I believe that even though most guys will give crap to the brand new Ensign and may say things that are disrespectful, I believe they would still follow any legitimate order if given. I have always insisted that being on submarines is hands down worse than being a SWO. Considering the fact that our happiness can boil down to a saying that most submariners have heard, as "Once the hatch is shut, there is only so much happiness on board, and the only way to become MORE happy, is to STEAL someone else's happiness" it is easy to understand that most people are just disgruntled and blur the lines of what is appropriate and what is not appropriate, especially when you have been beaten down for multiple years and start to feel that formalities and pleasantries are just a luxury that fall way behind operational commitments, maintenance, and watch standing.
Maybe Spekkio and myself have 2 bad eggs within our community, however, we are a small community and ever other nuke I have met or known, has pretty much given some sort of example similar to the one that Spekkio describes. It is unfortunate and hopefully it will be changed one day, however, I really do believe that the submarine force has a special atmosphere about it, that is unlike any other community in the rest of our military.