Most of the freelancers I know only did occasional gigs (most were either students or designers) and having to pay for monthly tax wasn't really an option as they didn't make that much.
People with 'agencies' have no tax debts, so they aren't really the issue here.
Generally, taxes for public services are paid even if you don't use them — it's the nature of the beast. Many people with decent income in Serbia almost exclusively use private healthcare because of the annoying see-a-GP-to-be-scheduled-to-see-a-specialist-in-several-months dance, yet they are obligated to pay for it.
But sure, it still feels bad for whoever has to pay (it's like a car loan that you want to pay off, and you still owe more than what the car is worth at that point: feels terrible, but that's your legal obligation).
Are freelancers considered employees here?
They are, however, not treated as employees (which have a lot of protections like minimum hourly wage, maximum working hours, maximum daily and weekly overtime hours, minimum number of paid vacation days, sick leave coverage at 60% of salary...). For freelancers, this does cause trouble with the pension fund employees not wanting to count your contributions toward your pension, but it depends heavily on who deals with processing your forms.
I agree this should be fixed elsewhere too, not just in the case of back-taxation.
There were (and still exist) problems with pension fund contributions being recognized, but that's more on the pension fund to figure out (I've got 11 months of payments from 2011 that they are not registering because of this, which is why I switched to self-employment then).
But this is also ignoring the fact that all these years until early in 2020, Serbia had an extremely low-tax mode of operation for such workers: self-employment with taxation on a predetermined fixed "income" up to an actual yearly income of 6 million RSD (~50,000 EUR). For IT workers, who had the biggest tax rates in those arrangements, it was not more than 400€ a month, which is pretty amazing for up to 4500€ of gross income. This arrangement only required registration with the tax office and business registry that you are operating a self-employment agency.
Sure, those at the lower end or irregular income wouldn't benefit from it, but Serbian government is already mostly forgiving their debt for anyone with less than 500€ of monthly income, and spreading the debt over 10 years, which are the terms protesters are not accepting.
I also think it'd be acceptable to offer the same taxation rate to anyone who would have been eligible for self-employement fixed-tax if it is more beneficial, and the accumulated interest would be the only "penalty" for skipping taxes.
That way people who did pay taxes wouldn't feel disadvantaged over the ones who avoided them.