Rebases and merges don't work well together. By default, git rebase will get rid of merge commits. While there is an option to preserve merges (-p), it can lead to some strange behaviour while doing an interactive rebase - see BUGS section in git-rebase man page for more details.

I'd also argue that merge and rebase represent fundamental differences in what commits mean. The former being commits are history, and the latter being commits are features.