1) as far as I am aware rail does not pay fuel taxes - it is exempt like farm vehicles - when it did in the past it was reimbursed. The trucks on the road in general don't have that exemption (I think there may be one for remote areas but they aren't served by ail anyway)
2) the Rail Access fees are also a cost of doing business and written off against income as an expense at the end of the year so no different to rego or any other business expense
3) The point was the rail industry has total control over its corridor (yes there are level crossings but you don't share every inch of your working area with other vehicle drivers that don't know/care what they are doing.) The average person doesn't expect to be able to fit rail wheels to their car and drive down the railway line yet they expect to be able to purchase a pushbike and ride it on the road without knowing the rules. The trucking industry has to.
4) Yes motorists pay rego etc that was part of my point. There were special levies in Victoria put on road diesal fuel to fund the Ring Road as a truck corridor. Back then about the only vehicles using diesel on the road were trucks so effectively trucks paid for the ring road (or 99% to allow for the occassional diesel 4wd) but when it opened it was opened for all road users.
5) I believe trucks should pay their way but so should cars, 4wd, motorbikes, pushbikes etc. I have a couple of restored vehicles that do about 2500 miles each in a year. I pay rego for both of them at the same rate as my wife's car that gets used daily yet they would do less damage as they cover fewer miles. There is no easy way to determine usage that some determined people couldn't get around. (eg when FBT was first introduced the tax office considered Utes and 4wd were exempt as company vehicles as they were considered to be needed as part of a trade. As a result accountants, solicitors etc started buying utes and 4wd to avoid the tax. The Tax Office changed its ruling so that all vehicles are subject to FBT to close this loophole)
6) I believe the funding (whether through fuel taxes or grants) should be proportionate to usage to be fair. When the rail industry starts caring about its customers in the way most trucking companies do there will be a swing back to rail. People don't like being treated like dirt. There is also the issue that almost everyone in the rail industry drives road vehicles but not everyone who drives road vehicles travels on trains - often for legitimate reasons and sometimes through laziness and fear.