In order to transmit from a country, one must have a license to do so, with the exception of some spaces without specific owners, like WiFi's 2.4 GHz that allows small narrow transition can work. It is common to have to pay for the bandwidth for each country. Some countries are pickier than others.
All that being said, it is perfectly normal and reasonable for India to request a license fee for the use of the bandwidth in their country. If SpaceX doesn't secure that, they can't install a ground station nor sell their service in the country. The law for small satellite providers is a tricky patchwork of each country needing licenses to transmit. I couldn't begin to tell you how the license process will go for India, but I can tell you they are certainly allowed to request this fee and other restrictions.
Of some note is they can't really regulate the satellite transmitting over their country, only the people on the ground transmitting to it. If a satellite happened to be over India, or any country, a person on the ocean in international waters could transmit to said satellite with no legal problems, assuming they were on a ship with a country registered to communicate with it, and the satellite could connect to a ground station outside of the country where it could connect to the internet.