While expressing thanks is definitely an admirable human quality and should be lauded, it frankly does not provide value to the other people viewing the page. Part of the problem, I think, is because "comments" on Stack Overflow have a different meaning and context than 99% of the web. They don't exist for some sort of "social" experience, but as a means of coordinating improvement to the content.
Maybe SO could do better to communicate that difference. Educating new users is one of the biggest challenges in the face of the eternal September that SO receives.
I agree that a comment consisting of nothing more than "thank you" isn't particularly helpful, but a "thank you" + some twist or application tip is interesting and valuable. Sadly, some SO-cops just see the words "thank you", ignore the rest of comment and then immediately recite the rules and/or delete the comment.
As for SO communicating the difference, I think they already do. Their problem is that people like me _deliberately_ ignore "the rules" and post whatever we think is appropriate-- the mods just can't keep up.
If that happens, then the mod is out of line. But what can SO do to prevent that behaviour? If you have ideas I'm sure the community on Meta would be more than happy to entertain suggestions, that's how the platform evolves and grows.
Those comments might get removed later, but saying "trolls are everywhere" is too pat when the people abusing new users are very visibly established, popular members of the community. Getting attacked by a random throwaway account is a very different feeling than getting attacked by someone up near the top of the totem pole.
"You should expect comments to get deleted.
If they are oh-so-important, they should get rolled into the post they are commenting on. At which point they are obsolete."
http://meta.stackoverflow.com/a/255140/592746
So, your problem, clearly, is that you think your "thank you" is "oh so important." If your ego wasn't so big, you'd get that.
I don't have "a problem".
I use stackoverflow quite productively, appreciate its utility, and help folks out with answers when I can. I've gotten acclimated to the rudeness but I wish it were a nicer place.... more skeet less passant.
[Edited for snarkiness.]
As much as I like (and heavily use) SO, it has a real problem with making people feel like shit when asking, answering and commenting.
There are people who are exemplary in their politeness and helpfulness like the top-contributor, John Skeet. There are also quite "mean" people like Hans Passant (also super-high score). I wish more people would use the really fantastic users like Skeet as an example of how to behave.
"Game-ification" strategies in social networks like SO tends to attract uncharitable, persnickety rule-zealots and this seems to have been re-enforced over the years.