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The problem with plugins is that they create a dependency on a third party -- OFTEN by authors doing it for a hobby or for free. And then you now rely said third party author to keep their plugins current. Plugins are likely the #1 reason for problems with Wordpress sites during an upgrade, themes are probably second. Not to mention that every plugin you use -- even those not activated -- add to a server overhead and external calls (such as checking them for upgrades).
Thus, for anyone with the ability to do so, removing as much reliance on third parties to make your site work is not a bad thing. Certainly for something as simple as backups, database dumps, and rsyncs, using native command line tools like tar, mysqldump, and shell ftp, would be more efficient overall.
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