There is flag on both submissions and comments. There is downvote on comments, but not on submissions. The "Reply" link is deliberately delayed on deep threads to help mitigate flame wars. These are all well-known features.
I agree it is not obvious to those who first come across these things. However, it is very well-known to anyone who searches for the countless threads about this very issue. Sadly, most people just ask the question without first researching the issue, and that then prompts several demonstrably incorrect answers.
It's also in the FAQ and the guidelines if you read hard enough, but some of the subtleties of the questions are not explained there (probably because they were fluid for a while).
