tl;dr: Sometimes, people don't try as hard as they could to be nice. If being nice is not a terminal value for you, here are some other things to think about which might induce you to be nice anyway.

There is a prevailing ethos in communities similar to ours - atheistic, intellectual groupings, who congregate around a topic rather than simply to congregate - and this ethos says that it is not necessary to be nice. I'm drawing on a commonsense notion of "niceness" here, which I hope won't confuse anyone (another feature of communities like this is that it's very easy to find people who claim to be confused by monosyllables). I do not merely mean "polite", which can be superficially like niceness when the person to whom the politeness is directed is in earshot but tends to be far more superficial. I claim that this ethos is mistaken and harmful. In so claiming, I do not also claim that I am always perfectly nice; I claim merely that I and others have good reasons to try to be.

The dispensing with niceness probably springs in large part from an extreme rejection of the ad hominem fallacy and of emotionally-based reasoning. Of course someone may be entirely miserable company and still have brilliant, cogent ideas; to reject communication with someone who just happens to be miserable company, in spite of their brilliant, cogent ideas, is to miss out on the (valuable) latter because of a silly emotional reaction to the (irrelevant) former. Since the point of the community is ideas; and the person's ideas are good; and how much fun they are to be around is irrelevant - well, bringing up that they are just terribly mean seems trivial at best, and perhaps an invocation of the aforementioned fallacy. We are here to talk about ideas! (Interestingly, this same courtesy is rarely extended to appalling spelling.)

The ad hominem fallacy is a fallacy, so this is a useful norm up to a point, but not up to the point where people who are perfectly capable of being nice, or learning to be nice, neglect to do so because it's apparently been rendered locally worthless. I submit that there are still good, pragmatic reasons to be nice, as follows. (These are claims about how to behave around real human-type persons. Many of them would likely be obsolete if we were all perfect Bayesians.)

It provides good incentives for others. It's easy enough to develop purely subconscious aversions to things that are unpleasant. If you are miserable company, people may stop talking to you without even knowing they're doing it, and some of these people may have ideas that would have benefited you.
It helps you hold off on proposing diagnoses. As tempting as it may be to dismiss people as crazy or stupid, this is a dangerous label for us biased creatures. Fewer people than you are tempted to call these things are genuinely worth writing off as thoroughly as this kind of name-calling may tempt you to do. Conveniently, both these words (as applied to people, more than ideas) and closely related ones are culturally considered mean, and a general niceness policy will exclude them.
It lets you exist in a cognitively diverse environment. Meanness is more tempting as an earlier resort when there's some kind of miscommunication, and miscommunication is more likely when you and your interlocutor think differently. Per #1, not making a conscious effort to be nice will tend to drive off the people with the greatest ratio of interesting new contributions to old rehashed repetitions.
It is a cooperative behavior. It's obvious that it's nicer to live in a world where everybody is nice than in a world where everyone is a jerk. What's less obvious, but still, I think, true, is that the cost of cooperatively being nice while others are mean is in fact very low. This is partly because human interaction is virtually always iterated, (semi-)public, or both; and also because it's just not very hard to be nice. The former lets you reap an excellent signaling effect:
It signals the hell out of your maturity, humility, and general awesome. If you spend as much time on the Internet as I do, you read a few online content publishers who publicly respond to their hate mail. It can sometimes be funny to read the nasty replies. But I generally walk away thinking more of the magnanimous ones who are patient even with their attackers.
It promotes productive affect in yourself and others. The atmosphere of a relationship or group has many effects, plenty of which aren't cognitively luminous, and some of which can spill over into your general mood and whatever you were hoping to use your brain for.
It is useful in theoretical discussions to draw a distinction between being mean to someone and doing something that's seriously morally wrong, but this line is fuzzier or completely absent in human prephilosophical intuitions. If you are ever troubled by ethical akrasia, it may be easier to stave off if you try to avoid delivering small slights and injuries as well as large violations.
It yields resources in the form of friendly others. Whether you are an introvert or an extrovert, other people can be useful to have around, and not even just for companionship. Compared to indifferent or actively hostile neighbors, it's an obvious win to be nice and win what goodwill you can.
It can save time - often yielding a net benefit, rather than wasting time as is sometimes complained. For instance, if a miscommunication is made, a mean response is to interpret the misstatement at face value and ridicule or attack - this can devolve into a time-consuming fight and may never resolve the initial issue. A nice response is to gently clarify, which can be over in minutes.