Coffee is, on the average, good for the health for most people. (But tea is an ok replacement.) http://en.wikipedia.org/wiki/Coffee_and_health#Benefits Do make your coffee with paper filters. [Edit: If you don't want to read the reference... paper filters removes some chemicals which are bad for cholesterol levels.]
Pointing out the long-term benefits of something without acknowledging either the long-term or short-term(which aren't really short-term if you continue to use it in the long term, but simply take effect sooner) costs doesn't justify any conclusions about whether the benefits typically outweigh the risks.