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No. Sigil will quite happily work with files in root or in arbitrary folders. It just requires that url links be relative and match the physical file paths.
If you had stylesheet.css in the root of the epub alongside your xhtml file then your link to your font files from the css is wrong because you can not legally proceed up one directory out of the root directory and back in, and also that would then be inconsistent with the manifest href for the stylesheet.css file from your content.opf.
All relative links must actually follow the physical folders and paths in the epub and match the layout as defined by the content.opf manifest.
Turning on full file paths in Sigil's BookBrowser will enable you to see actual epub root relative file paths so you can make proper relative links if you choose to do so manually but it is probably easier to use Sigil generate the correct links/hrefs/urls for you.
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