Remember to count it as moving vehicle space, with whatever buffer is allotted to each, since that's what really counts. Granted, it's a very different number whether we're talking shared lanes versus dedicated lanes.  That's what complicates the issue a lot. Where bikes and motor vehicles share the same lanes, I'd agree that bikes account for a small % of the space and thus should collectively pay only a small % of the usage-based funding.  

But it's a whole different matter when valuable and costly road/path space is used up to give DEDICATED bike space. Then we're talking about the width of the dedicated lane as a % of the width of the whole road. Which can be upwards of 10-20%, depending on the configuration. Or 100% for a separate bike path. There's only a limited number of dedicated bike lanes/paths, of course, although that percentage is growing too.  

What the actual fee/tax should be after crunching all those numbers is something neither of us really know without that data.