What is the point of tying taxation to plain mileage then if you don't propose on charging differently for different miles? Fuel duty does basically the same thing.
Because the Treasury is losing a source of tax income that it needs to replace. The "do nothing" option is not to retain fuel duty, but to see fuel duty dwindle to near zero.
Going back to brass tacks, fuel duty is hard to avoid and cheap to collect. It does not distinguish between type of road used, but otherwise penalises those who drive high mileages and/or inefficient cars due to the amount of fuel they use.
A per mile charge largely replicates that, whether flat rate or banded by car type/efficiency. A tolling mechanism is fundamentally different in nature, and demands far more resources to collect efficiently. It also risks perverse outcomes - if different road types are tolled differently (presumably higher tolls for higher grade roads), then you risk diverting traffic away from those roads. We already see that with satnavs diverting traffic to roads that aren't designed to cope - this will further boost those algorithms. Keep it flat rate in a car, and you maintain the current general pattern* that drivers focus on time and convenience, rather than trip cost.
An example. When I drive from Grantham to Lincoln, I normally go A1/A46. It's fast, and it's convenient, but it's also longer than either A607 or the back road through Marston and Brant Broughton. Put tolls into the equation, where my journey cost is not just about distance but also rate per mile, and those other routes stop being a nice country drive and start to become alternatives. That undermines the purpose of the trunk road network.
* - we will all know someone (or even be someone) who calculates the cost of each trip to the penny, and decides purely economically. But that is the exception rather than the rule, and it is the general behaviour of the population as a whole that will matter.