Sometimes the rejection reason indicates something the reporter didn't address, and re-flagging with a (hopefully better/more detailed) rejection reason helps. As an example, maybe I'll flag as Not an answer, get the response of "don't flag for invalid content" and then reflag saying that while the answer may be well formatted and explained, it's attempting to answer an entirely different question from what the OP is asking, and is therefore not an answer. That's a case that a lot of mods don't often see when looking at the answer in isolation, and so occasionally needs to be re-flagged.
Another issue is that mods can't reject individual flags. Rejecting one flag rejects all flags for that post. If someone flags as not an answer, and another as spam, and the spam is rejected, the not an answer goes with it, even though the post may well be not an answer.
In the rare cases of true abuse of the flagging system, in which a user is constantly re-flagging a post when it's clear that there is no problem with it, the mods have tools for dealing with the problem. For one, the flag weight will go down (so their flags just won't be read as quickly) and they could resort to more significant consequences in cases of extreme abuse.