Primarily because businesses are fictional people. Being somewhat incorporeal, businesses historically were notoriously hard to sue. How do you serve your summons on something that doesn't exist? If you go to the main office and can't get any further than the receptionist, can you serve her? What if you only have a brand name and can't find the corporation that owns the brand?
Who would you sue if you were poisoned by Kashi brand cereal? It's Kellogg, by the way. Have a problem with Ben & Jerry's ice cream? That's Unilever.
To solve this problem, the government mandates that all corporations keep on file with the state a home office and responsible person. Furthermore, all business names must be registered so that the true owners of the business or brand can be found. The State is authorized to accept service of legal papers on behalf of the business. So, no one ever has to have any difficulty finding the corpus of the business. It resides with the state.
These government services are not free. It costs the government money to register businesses, keep records, accept service of process, and forward papers on to the business' office.
In addition, the government can generate lists of businesses in certain categories in order to improve compliance with regulations. How do health inspectors know where to go? Do they just drive around?
To offset these costs, there is a small fee for service. This is a "tax" only on those who use the service.
It all seems pretty fair to me.