Currently the interface provides no simple mechanism for: "I like the post, but feel the payout is excessive, so I'm going to vote against it using my own influence to bring the payout down, thus leaving more payouts for others." If the flag had a "reason" option which included some text (it could even just auto-post a comment to that effect if we didn't want to change the blockchain structure for the new meta data about the flag), then I think it would solve so much confusion here. It would even still follow the "abuse prevention" intent a flag implies.
I can't speak for others but 100% of the time I post a comment when I downvote for any reason (and sometimes to state a reason when upvoting if I have a reason worth noting other than "I like it and want to see it rewarded"). Obviously we can't force everyone to do that, but I definitely encourage it.