It's hard to say what your problem is without seeing your RTF. All I can say is it works for me, perhaps your conversion settings need changing.
The attached zip contains 4 files:
- a sample RTF containing chapters (styled with 'Heading 2') and footnotes
- an epub created by a RTF-to-EPUB conversion
- an HTML file created from the RTF by doing an MSWord File - SaveAs - webpage-filtered
- an epub created by a ZIP-to-EPUB conversion, after importing the HTML file into Calibre (which changes the .htm file to a .zip file)
Both conversions used the same conversion settings.
Both epubs contain a working TOC when viewed in the Calibre Viewer.
Only the ZIP-to-EPUB conversion retains the footnotes hyperlinks. As a general rule saving your RTFs as HTML (webpage-filtered) before importing to Calibre will give a 'better' epub conversion.