One solution is to simply treat everyone equally and not give anyone a tax break.
I know this is not what most people think, but in the context of good governance, my view is that no (legal) behavior is any more or less meritorious than any other.
There are lots of perfectly legal things that are bad for everyone if too many people do them (the tragedy of the commons). Trying to reduce bad things happening to citizens is arguably the entire purpose of government.
Never really noticed it until I started a new job and they were pitching all these federal and company commuter benefits and didn't see a single one for bikes.
But hey.. my work has a nice locker room that makes biking possible so it's not all bad! I also ride about half the way on bike paths under high voltage lines so I do get some benefits :)