Taxation of a common good (land use, water use, frequency use, air pollution) is normally done because somebody makes money by using that common good, and the government want to have its share of the profits. That's why commercial vehicles pay road tax and so forth.
If a commercial operator (a cellphone provider, say), gets exclusive use of a certain frequency range, and uses that to make money, it's very logical that the government wants a share of this.
Aviation doesn't make money from using the aviation frequencies. Instead, it's a safety tool. Putting a tax on it would be like applying taxes when somebody dials the emergency number.