Bicycle registration fees could just reflect the same portion of the cost that bus or train tickets represent. And I think that bike lanes cost more than you think. Some lanes take up whole lanes of traffic, removing fuel tax revenue from those lanes. Others are dedicated lanes that are built in addition to the regular road.

But that is beside the point. You said that bikes lanes should be looked at as part of the overall picture. I agree completely. In that case, you can't single them out for special consideration. Otherwise, using your logic, since I have multiple cars, I should be getting my light rail tickets for free since I am already paying taxes with my cars. Trust me, I will gladly accept that $9 per day in savings on train tickets.