Hiller is a pretty equal opportunity hound of state politicians. Definitely not a cheerleader for Baker's failure or a holder of sour grapes for Coakley losing.
It's a political analysis article. Hiller isn't saying that Baker should be blamed for it, he's saying that Baker will be the official with the bull's eye on him now that he can't use Scott as a foil. That could well be incorrect analysis, but he's not assigning blame to Baker at all.
As a general aside. Assigning blame to anyone at this point is a pointless pissing match. Obviously the situation isn't Scott's fault. But it's just as asinine to pin the woes on Baker. Even if he was responsible for foisting a chunk of Big Dig debt onto the MBTA, that is also not the root of the problem. It's a problem, and was a mistake, but it's not like Baker is the guy who personally crippled the T. Generally the blame belongs to all of us, through our votes, and more directly to our legislators. The broken MBTA is a product of a general failure of governance from the General Court, several Governors, citizen referendums, and the MBTA's administrative policies over the last 25 years. There's plenty of blame to go around, and getting into a pissing match over who's more to blame is a waste of time. Just accept that it's broken because we broke it, collectively, as a Commonwealth. Once we move beyond the past and just accept that it is what it is, we'll be in a better position to look forward on how to mend it, rather than backward at who we are pissed at.