I think the discrepancy with FHWA is due to different ways of grouping things. Now, the report I cited was covering the overall highway picture from Interstates down. But let's look at Massachusetts more closely.
The T4MA report has a nice diagram showing the inputs: $660 million state gas tax, $500 million registry fees, $302 million from sales tax, $350 from tolls, and $10 million from other. Generally speaking, most people consider "user fees" to be gas tax and tolls. But let's add registry fees for argument's sake. I cannot imagine any reasonable way that sales taxes or property taxes are user fees. That puts us at just about $1.52 billion in "user fees" for our purposes.
Of that, $1.06 billion goes to debt service, $360 million goes to Mass Pike and Tobin bridge, $151 million goes to MassDOT operation. Then some goes to other things like MBTA, RTAs, and snow/ice removal.
$1.52 billion revenues, $1.57 billion expenditures. And that hasn't yet accounted for things like
Chapter 90 Road Funding thru Cherry Sheets, which amounted to a $200 million subsidy most recently, and $155 million in the previous year.