In case you were wondering about this, the short answer is you still can't do it (and yet without this "bailout" Citibike still somehow remains in operation).
Here's the long answer.
The bike commuter benefit was the brainchild of Rep. Earl Blumenauer (D-OR) and was included in tax extenders legislation that passed Congress in 2008 as part of the bailout bill - the same one that created TARP - and signed into law by George W. Bush. Oddly enough, Blumenauer voted against the bill, because it was not paid for, and Republicans voted for it even thought it wasn't. Such is politics. This was before bike sharing was really a big deal - CaBi had launched only a few days beforehand - and so the bill didn't mention it. Since then, bike sharing became a thing that people actually use to commute to work and they want to use their Bike Commuter Benefit (if they get one) or their transit benefit to pay for their membership and fees.
In 2013, the IRS was asked if it could "adopt bike share as a qualifier for the Transportation (Commuting) Benefits program under the Fringe Benefit Exclusion Rules for transit," the same rules under which employers can give tax free transportation benefits to employees. But in July of that year, they said no, because bike share is not mass transit. They also said that bike share was not a qualified bicycle commuting reimbursement, which one could pay with the bicycle commuter benefit, because those were specifically limited to "expenses for the purchase of a bicycle or bicycle improvements, repair or storage."
So, a legislative fix was needed.
In 2014, Sen. Charles Schumer (D-NY) had an amendment added to the EXPIRE Act, an act which would extend many tax breaks that had expired (just as was the case in the 2008 legislation), that would modify the list of qualified transportation expenses to include expenses associated with the use of a bike sharing program. That amendment passed, and there was much rejoicing. The bill was passed unanimously out of committee, but was filibustered in the Senate in a fight over amendments.
In 2015, Schumer tried again. This time the vehicle was the Tax Relief Extension Act, which again dealt with tax extenders. It too got out of committee, but has never come up for a vote. Many of the tax extenders it dealt with were rolled into the Consolidated Appropriations Act of 2016, the so-called omnibus bill, but not the one dealing with bike sharing.
So, bike sharing still can't be treated as transit or as a qualifying bike commuting expense for tax purposes, no matter how many people use it for commuting. And it appears that will continue to be true for the foreseeable future.