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xdg-open /run/user/1000/gvfs/ftp:host=smart,port=5555,user=u runs chrome.

How to make it run nautilus instead?

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From man xdg-open

xdg-open opens a file or URL in the user's preferred application. If a URL is provided the URL will be opened in the user's preferred web browser.
...
xdg-open supports file, ftp, http and https URLs.

The man page states that as long as the target is a recognized URL it will always use a web browser. This looks like what you want is not possible
(apart from registering nautilus as your favourite web browser whis is a bad idea™ )

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