As far as I know Stack Exchange sites are meant to be based primarily on up-voting. If a post deserves a down-vote isit should be so bad that the voter is prepared to lose 1 reputation. Thus, I think that losing reputation on down-voting an answer is to restrain down-voting to a reasonable level and promote up-voting as the primary voting method (note that there are three alternatives when it comes to voting: vote up, vote down and not vote). Also it will work against answerer'sanswerers voting down the competing answers.
Finally, in the ideal case you down-vote an answer and also post a comment so that the answerer may improve their answer accordingly and then the answerer improves their answer and you remove your down-vote. In that case the quality is improved and you regain the lost reputation.