I am pretty sure that they are referring to the three miles of road between the gate and the trailhead. More guidance on the issue here:
Biking on the Pacific Northwest Trail
Look under Prohibitions. Most of or all the trail lies inside the Stephen Mather Wilderness. There is an outside possibility bikes are allowed from the trailhead to Thunder Campground but I have my doubts.
More:
http://www.nps.gov/noca/planyourvisi...e%2009_web.pdf
Look on page 2: "Mountain biking is not permitted on park or forest trails except where developed for that use. However, riding is allowed on roads."