Amazon contracts out their delivery services. But let's assume you mean UPS, USPS or even if Amazon were itself making the deliveries.
Don't those trucks pay registration fees, tolls and fuel taxes already? Aren't those taxes and fees designed to maintain the roads?
Are you suggesting that there's some other tax Amazon should be paying in addition to the fees they already pay?
This concept that corporations somehow benefit from the roads more than the consumers who purchase their products and individual drivers who utilize those roads is incomprehensible to me. Everyone who uses the roads benefits. Those roads are supposed to be paid for by the various fees (fuel taxes, tolls, excise taxes, licensing taxes, etc.) extracted.
Further, your argument that a road in Iowa is not very beneficial to a person in Florida has no meaning outside an interstate highway. The non-interstate highways in Iowa are paid for by Iowans and those non-Iowans who drive through Iowa, likewise for Florida.
You should also look at the study and what they considered a benefit - they looked well beyond income and looked at all government services.