There are a lot of sites with a . . . less technical bent than Stack Overflow, ones that involve and thrive on good subjectivity. This means that opinions play a more important role in answers, and it seems that everyone likes to hold opinions. People also have a tendency to see opinions they disagree with and refute them by many means . . . including long comment discussions. Therefore, to crack down on this, some sites are tough on comments, often through specific site policy.
Examples of sites where this sort of thing can be a problem include
. . . and others. Some sites are just bizarre - I couldn't begin to describe some of the weird comments I've deleted on Worldbuilding - and also invite discussion.
A review of comment policies across the network would be nigh impossible - or at least would take a large chunk of the day - but it should suffice to say that what with comments being second-class citizens, they're designed to disappear at some point, once they've served their purpose. For comments that don't do what comments are supposed to do (bad comment examples include answers in comments, stuff a la "-1. I disagree", and general unhelpfulness), mods are really only speeding up their lifecycle a bit. This reduces clutter and gives more space and attention to comments which are, for their brief period of time, relevant.