Federal funding for road projects (among myriad others) is being cut, so funding will have to come from somewhere.
If they really wanted to target drivers passing through the state as that claim, they should exempt hoosiers entirely from the tolls. But I think they're just blowing smoke, so their constituents won't get mad.
The alternatives, as I see them, would be increasing registration fees or gas tax. Gas tax increase is obviously a no-go, because people will complain about fuel costs rising. Higher registration fees could be possible since they've done it before on electric vehicles, but would be argued against as: reducing the ability of poor families to afford a car.
If I had my way, I'd exempt anything below 2 tons, since the heavier vehicles do far more damage. Then use 50% of the revenue to build a cycleway parallel to Kentucky ave, and another at mass ave to 21st and/or 30th.