From an Operations standpoint, having two conflicting package management systems is a huge headache. It's one more point of failure on production systems. The jpackage project was a similar effort which packaged oft-used Java libraries in RPM format.

Here is a thread (and related article) on HN about the problems with RubyGems: http://news.ycombinator.com/item?id=386036

Here is the official position of the Debian/Ruby-Extras team: http://pkg-ruby-extras.alioth.debian.org/rubygems.html

It has been a polarizing issue, as you can see.