The chief evidence of bias comes from PolitiFact's attempt to discredit Reason.com on ideological grounds--an intriguing move for an organization known to uncritically cite Guttmacher Institute studies when fact checking claims by abortion opponents. The Guttmacher Institute, of course, is ideologically attached to Planned Parenthood.
Most of PolitiFact's criticisms of the study promoted by Reason.com were quite weak, such as pointing out that data from the study showing cost overruns were not exclusively rail studies. While that's true, the cost overruns were greater for rail projects, so the supposed problem actually made rail look perhaps better than it deserved.
The key point of dispute concerns the responsibility for costs if the project stays in the red. PolitiFact argued that Florida's project provided adequate protections. Reason.com argues the reverse:
When Gov. Scott was making his rail decision, he knew that if Florida had taken federal money for the Tampa-to-Orlando high-speed rail system, one of the federal government’s rules clearly says that a state government can’t take the construction money and then stop operating the project it has accepted the money for. Under long-standing federal rules, the state would have to repay the federal grant money—in this case, $2.4 billion. If it didn’t repay the $2.4 billion, Florida’s taxpayers would be forced to keep the train running —at a loss— and be on the hook for the future operating subsidies. The U.S. Department of Transportation did send notice that it would negotiate over its repayment rule, but only after Gov. Scott had already announced his decision to turn down the federal money.I'll admit I'm not familiar with the cited rule, but it's easy on principle to imagine it exists. It could have helped Reason.com's case to include more information about it.
On the whole, Reason.com makes a pretty good case that PolitiFact failed to settle the issue.