Sometimes a post is controversial for one reason or another, and people want to debate it. Sometimes a side issue comes up and people want to discuss it. Are comments a good place to do this?
Comments are meant for suggesting improvements, asking for clarification, and so on. It even says in the box, before you start typing:
Use comments to ask for more information or suggest improvements. Avoid comments like "+1" or "thanks".
That's a relatively new feature, but it's been the idea all along. And it means information about or improvements to the post you're commenting on.
Comments are also meant to be at least potentially temporary:
Comments are temporary "Post-It" notes left on a question or answer. They can be up-voted (but not down-voted) and flagged, but do not generate reputation. There's no revision history, and when they are deleted they're gone for good.
A lot of comments are in some way directly useful, so they stick around. Others don't really need to persist. Yes, sometimes it is necessary to have a quick exchange of information in comments to work something out. And anything for the sake of clarifying/improving a question or answer is a good thing. But once things are resolved, especially if there was a long discussion, we'll often clean up and delete them.
And if the topic is something other than the question/answer at hand, comments are not the right place. This includes tangential discussions. If the conclusion is not something that could reasonably be edited into the post to improve it, comments aren't the right place. For back-and-forth discussions, try chat. If a discussion goes long enough, the site will even automatically try to get you to move it to chat. For a specific question about how the site works or the right way to do something, post on here on meta.
We're not totally un-fun, of course - you'll find some quick jokes, side notes, and so on, and that's fine. But we do try to keep things generally clean, and we're more vigilant about it than a lot of other StackExchange sites. The goal is that if someone finds the question/answer in a year, they can read through it and everything they read will help them. Many sites are content to just have a dozen comments on every post, and may not even have enough flagging/moderation to change that. We try to do better, keeping things tidy for our readers.
This is why we have a way to flag comments: as rude or offensive, not constructive, obsolete, or too chatty. If a user thinks a comment is any of those things, they can flag it, and assuming they've judged correctly, a moderator will delete it. If you find yourself frequently posting comments which are flagged/deleted, you're probably using comments for the wrong purpose, creating unnecessary noise for other readers, and giving moderators more cleanup work to do.
And one final side note: of those reasons, "rude or offensive" is by far the worst. It's one thing to add some noise to the site and make a mod clean up after you, but offending other users is crossing a line. No one here will take kindly to it.