It depends how the book is formatted. Fonts can be defined either as they "Body" of the html, or in the style of the paragraph. Kobo font setting will overwrite the 'Body' font, but not the Paragraph style.
So, your available choices:
Use calibre to convert the book, (if already an epub, you can re-convert to epub), but but a check mark on "Fonts" in the Look & Feel -> Styling tab.
Alternatively, you can install the KoboTouchExtended Plugin in Calibre, and therefore send books to the Kobo in Kepub format. I have a lengthy post in the Tips and Tricks thread with a more comprehensive instruction that also allow the use of Full Screen Mode.
And finally, you can use the Patches to patch and customize your firmware. I believe there are options in the patches to enable always using user selected font.
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