It does not bother me that unpopular stuff is downvoted (who really cares?), but it's a real dynamic. You said it yourself, if you want to craft a comment to be popular, there's a way to do that; it's not especially hard to figure out what to say if you spend time in various forums.
Maybe the issue with the upvoting system is it gives more credence to a baseless comment having value or being correct, when it's about popularity. From a social perspective it seems like a really great way to spread misinformation. Why would you not care about that?
In my opinion there is a system of homeostasis that exists in internet comments. When a popular wrong opinion gets large enough it is a huge low hanging fruit. There is a race to be the first one to debunk it and cash in all the delicious "well, actually" karma. Go look at the top comment on any given hacker news thread. I wouldn't be surprised to find an overwhelming number of "well, actually" child comments immediately below them.
Furthermore, popular anonymous comments are nice but the real world still operates on reputation based media. A popular comment might inspire a reporter at a media source of record to write an article about it but you can bet their first order of business is to cut out the rhetoric and make the opinion seem as objective as possible. In many cases once you cut out the rhetoric of a baseless popular opinion there is no article, so on a larger social scale the popular comment basically dead in the water. A firstname-lastname reporter is thinking in terms of a career, not upvotes. That's why when you read the sources of a non-fiction book you see The New York Times and not The Slashdot Comment Section.
* Also I just want to clarify that the "someone" in my original reply to your comment was not a veiled accusation, I literally meant someone (anyone). It was not a passive aggressive attempt suggest that you are getting too emotionally involved with your comments. I merely meant that a lot of people (myself included) get too caught up in thinking that 1. they are objectively right and 2. lack of recognition of this fact must mean that the system is broken.
A popular opinion doesn't make other opinions invalid and I think that's a mistake many people read into the situation because they're too emotionally invested. On top of that it completely ignores the countless variables that go into a top comment on a popular forum.
The best advice I can give is either 1. Don't take the unpopularity of your contributions so seriously or 2. take it so seriously that you're willing to understand how to game the system to MAKE your "objectively correct" opinion popular.