It does. If your argument for the legitimacy of collecting tolls from a waterway is that you have built it, and hence you are eligible to collect tolls for your investment, then the Suez Canal is also not eligible for that.
State the international law that defines what rights Iran has in its territorial waters

Even the UNCLOS, which Iran has not ratified, disagrees with what you said. Countries are allowed to exercise traffic control over their territorial waters in time of war. It is pretty explicit.
Different countries are charged differently. If you play nice, you can be exempted from the toll. Iraq, China and Russia are already receiving serious discounts. Pakistan is getting discounts too, but not as much as Iraq, China or Russia.