I dunno. Rotmensen is just too bizarre to take seriously, unless the intention is to show the Fed (or at least United Earth) being run by thought police.
I don't find him bizarre - he's simply the unfortunate union of two behaviours that are very much already confirmed in reality (at least in my experience) and one that's confirmed as a part of the Trek universe.

First, as
Nerys said, he's an academic who is caught up in his own "ivory tower". I've been at a well-established university for three years now, and I can certainly say there is a real tendency for these otherwise supremely intelligent people to be really quite blind to the world outside, or to perspectives not their own. They make assumptions a lot as well. Usually, that's a bit irritating but nothing majorly disruptive - because I've been lucky enough to have a string of really welcoming and friendly directors and supervisors.
Everyone has their blind spots (which is part of what
Nerys is saying here, of course), and I just shrug it off (though I never feel truly at home there, and I really worry that universities are far more closed-minded and restrictive than they should be). Rotmensen, though, goes beyond that because he combines his short-sightedness with a pronounced aggression towards certain philosophies. In his case, he apparently views religious belief as detrimental, only responsible for holding back human progress or contributing to wars, and he clearly thinks it's a distasteful practice that should be abandoned. And when a cadet brings their religious devotion into his closed academic world it becomes an intolerable intrusion to him. How dare this backward dinosaur pollute Rotmensen's world with his (supposed) short-sighted metality?!

The irony is of course that Spirodopolous does not seek to impose anything, and it is Rotmensen's own unexamined intolerance that's the issue.
We all have our prejudices, as
Nerys again says, but when prejudiced beliefs are combined with aggression, that's when it turns nasty. And aggression is the response when someone feels their world has been intruded into. A short-sighted person like Rotmensen with his very closed, "ivory tower" existence, without input to challenge his assumptions or force re-examination...well, he'll feel intruded upon by pretty much
anything outside his narrow assumptions, and it's easy to end up with what we get: someone who attacks those who clearly do not deserve anything of the sort, and reads a personal, non-imposing belief system as an attack upon his world.
And Rotmensen's prejudice regarding religion isn't bizarre either - there are indeed people who believe as he does, that religion will inevitably result in book-burning and infidel-slaying and whatnot. And given the more secular society of Trek's humans plus their oft-repeated assertion that they're "evolved", it's easy to imagine that the idea of religion as a backward piece of baggage is actually more common in their world than ours. So Rotmensen, as I see it, is simply the meeting of three personal traits that are questionable but alone can be handled; put together, you end up with...well, this guy.
Also, finally, I think we should keep in mind that this was written for a "prejudice" theme competition, so it is going to be very upfront with it.
And, if I may say so, I really like the point that it is
humans towards which Rotmensen demonstrates intolerance; like many people in reality, he forgets that diversity has to include those of his own kind too - but interestingly enough those who otherwise preach tolerance often seem to have blind spots when it comes to those closer to home. That's one of the interesting wrinkles of the issue of prejudice that this piece is exploring. And Spirodopolous sees this and says "if you can't handle a human thinking and behaving in a manner you feel humans somehow shouldn't, then just pretend I'm something else - one of the many alien races who you don't judge like you do your own people".