That would certainly fit with the slightly slapstick bureaucracy image that the Ministry is given in the books. Their only method of funding is by handing out fines, so they constantly expand what they can give fines for, which necessitates greater numbers of staff, which costs more, which means they need to fine for new things again etc.

 

I also think fines and licenses are a great way to fund the ministry. I kind of think you could set up the ministry so that it screws over everyone, and so results in constant political unrest. I don’t want to sound weird, and sometimes I find it difficult to articulate my thoughts.
Somehow, in the Harry Potter universe, the old, rich and ancient families saw fit to engage in terrorism instead of political maneuvering, lobbying and so forth. To me, that means they had to be somehow disenfranchised enough somehow that they resorted to terrorism. Explaining them to be all evil might work for a childrens novel, but is a bit unrealistic in a world that is not painted in black and white.
I think the conflict is easier explained if you set up the funding for the ministry in a way that it screws over most of the people.
So, maybe unfairly taxing the exchange rate as was marvelously thought up in a higher post, and possibly a large range of licenses and fines.
And then find something slipped in a regulation that is bad for purebloods and old families. The rich people can bribe their way out, the others have to without, and nooners happy.
Think about it, Umbridge was extremely happy to concoct edicts and regulation after one another.
I think you need a license for crups and kneazles, which seem like the magical version of cats and dogs.Maybe expand on that. Say, rich purebloods have huge manors. Let’s tax and license them for every magical animal that’s on their estate, regardless if it’s domesticated or not.
Make regular and complicated updates to the building standards and warding, and have regularly check that, and make people pay for each update and change.

Swallow up branches of magic into the ministry that technically all could make themselves, declare it illegal without ministry oversight and soak up the revenue

 

They are funded by "donations" from Lucius Malfoy and his kind, of course.

 

Permits for things like enchanting and magical manufacturing might make sense. Would also create a scenario where people can make things for themselves if they are able to, but selling things is monopolized by means of bribing the ministry to issue very few licenses.

Other than that, while sales taxes are fair game, I don't see how land taxes would work. Most wizards live among muggles, and they can't exactly decide to demand taxes for some land just because it's being used by a non-muggle. Same for wizards living in isolated locations and constructing their own houses. So the only place it would be applicable would be magical settlements, and if that's the only place they were applied costs would be higher there and only rich people would be living there, which we know isn't the case.