For example, if one is frequently doing "fix after rebase" commits, then they are doing it wrong and are making a history which is much less useful than a seemingly more complicated merge based history. Rebased histories are only clean if they also tell a true story after the rebase, but if you push "rebase fixes" onto the end of your history, then it means that prior rebased commits no longer make any sense because they e.g. use APIs that aren't actually there. Giving up and squashing everything to one commit is almost better in this case because it at least won't throw off someone who is trying to make sense of the history in the future.

I think that rebasing has won over merges mostly because the tools for navigating git histories suck SO HARD. I have used Perforce at a previous job, and their graphical tools for navigating a merge based history are excellent and were really useful for doing code archeology.