Isn’t that the case with any fine collected by any government? Why are people suddenly so much against these types of fines when it’s the EU fining them?

Are you claiming that EU officials are illegally pocketing the collected fines for themselves, or do you just not know how government budgets work?

By this criticism, are we to understand that you're against all fines collected by the government? Everything from parking tickets to penalties paid for crimes, misdemeanors, felonies by citizens etc? If that's the case, that seems like a very fringe perspective, consistent only with "all taxation is theft" flavored libertarianism.

EU is a democratically accountable institution, in theory (and also in practice) voters are able to affect the way these fines are used, and how they're collected. Yes, these fines are not going to be redistributed into EU citizens' pockets, but they will be used in ways that will benefit EU citizens one way or another.