This is actually a problem with the component that sets default
applications (I think gconf), as described here:
http://radu.cotescu.com/2010/01/22/how-to-set-nautilus-as-default-ftp-
application/
That also contains the solution.
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https://bugs.launchpad.net/bugs/784007
Title:
Nautilus, after upgrade from 10.10 to 11.04, opens ftp bookmarks in
default web browser
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