It seems the points cost is (at least in part) to help prevent tactical down-voting, a process of pushing one's own answers further up the rankings by down-voting its rivals. Answers which already have a lot of up-votes tend to attract more votes thus by being at the top quickly one can get more votes (some people care far too much about their points - personally I am proud of the points I have achieved because they tell me that people value my contribution and thus there is a benefit to my getting involved with BiologySE, but I don't see the point of getting tactical, what importance do the points really have - no one is going to employ you on the basis of your BiologySE rep!!).
Perhaps an improvement of the system would be one which can recognize tactical voting - I'd suggest that if a post has a score of -2 or lower, or has accumulated several down-votes but remains positively scored (e.g. has total score of 5 from 10 up-votes and 5 down-votes) then the down-vote should be free of charge. If a user down-votes something which has no other/only few down-votes (the threshold number of down-votes would have to be based on the specific needs of the SE site - something is far more likely to accrue one or two tactical down-votes on a large site like stackoverflow due to the number of users and hits) they get charged (but it is refunded if others agree).
Subsequently it would offer a viable option when the post is not good (worthy of down-voting) but not worthy of flagging (flag likely to be declined).