Your account isn't penalized.
The story you submitted didn't get any special moderation penalty. It got a mild automated penalty for being NSA-related (this has been in place for over a year) and then it got several user flags. By the time you complained about its rank dropping, it was already rising again. This is what happens when some users upvote an item while others flag it.
The HN guidelines say that most stories about politics are off-topic. The story you posted is pure politics. The thread immediately degenerated into accusing Muslims of being fifth columnists and rapists. That's the kind of thing that happens in pure political threads. (That one is particularly dismaying, though. If there is anything less desirable on Hacker News than religious flamewars, I can't think of what it might be.)
The HN guidelines emphasize that Hacker News is not all tech-related. Stories of intellectual substance are welcome on all subjects. A scholarly paper about brain research is plainly within this scope, even if it isn't a great scholarly paper about brain research.
The HN guidelines ask you not to post complaints about moderation to Hacker News itself, but instead to email hn@ycombinator.com, where we are happy to answer questions. We can't always reply immediately, but we do reply.