StackOverflow Meta - Why do you lose reputation for down-voting?
Main points of top answer copied here:
The motivation behind it is to put emphasis on up-voting or not voting at all. This way, down votes will carry more weight and it will also prevent users from abusing the system by down-voting excessively.
According to what Jeff/Joel discussed on the SO podcast, they wanted to find a way to discourage users from down-voting for less legitimate reasons (say a pro-Java developer down-voting everything remotely related to .NET or the like).
Additionally, if the post is deleted, you should get that rep back.