Similarly like the weight of an upvote might be different from 0.00001$ till 100+$ depending of Steem Power, the same way it works for flag.
Suppose your post generated 10$ Reward. If I flag your post it only cost you 0.01$. If a whale flag you, not only your reward will be zero , your rep score will also suffer.
For me the best way to deal with flag would be just ask the person who did it what's wrong. Flag can be removed during first 24 hours.
The other way is, if someone with equale high SP upvotes you - it recovers your reputation . You can always ask for help using #steemitabuse tag.