It's not this specific decision, but this category of decisions. The EU seems to constantly legislate on "small" things that piss off some subset of the population in a country. Eventually there's a large enough number of annoyances that a majority of individuals are bothered by.
To take an arbitrary example - increasing the age required to obtain an unrestricted motorcycle license.
On the face of it it's not that significant. No-one really cares about this apart from in the abstract. It reduces death rates, and from that perspective it's a good thing.
But there's some small bit of the population that is now pissed off by this, you've told them "wait until you're older", and they don't like that and vote against you.
(It certainly annoyed me at the time despite already having a full licence and already being above the new cut off. No, not enough to vote Leave. I like my citizenship.).
Now multiply that by lots of issues which affect different people.
You don't consider this kind of crap to be one of the reasons why people voted for Brexit?
I voted for Brexit not because of most of the commonly touted but because of the breathtaking arrogance of the EU leaders. If you followed the series of referenda all around Europe regarding the EU's policies, you will see that in almost every instance the popular vote went against the EU, only for member countries politicians to ignore the peoples votes.
Britain is simply a country whose leaders promised to leave the EU if the public voted against it, and as far as we can see they are committed to honouring that promise.
It was the EUs handling of Jorg Haider's party's election victory that decided Brexit for me, ie about 8 or 9 years before the Brexit vote, and FWIW I am not white. Don't assume that all the reasons usually touted were the cause for the vote for Brexit.
Honestly, having read many EU standards, they are usually some of the most sensible, reasonable legislation you could ask, on both the consumer and producer side. Most silliness that gets blamed on them is either willfull misinterpretation of the rules ('EU says banana must be straight!'. No, EU says bananas must not be misshapen (by, for example, having a 90 degree bend in the middle of an otherwise normally shaped banana) if they are to be classed above a certain grade), or excessive risk aversion on the part of companies (usually driven by lawyers).
They claim their law applies to their citizens. Especially on the internet, where a company can be 'based' wherever will regulate them the least, this is a reasonable compromise.
National governments do crazy stuff like this constantly too. They also do useful things. So does the EU. The case (or at least this case) against the EU is pretty much the same as the case against all governments.
The right question isn't "does this organization do crazy things?" but "do the good things outweigh the bad, or the other way around?".
The other thing is that I think a lot of the "EU does crazy things" narrative is deliberately, and dishonestly, pushed by people who are more interested in making the EU look bad than in the truth. (I am not suggesting that sarcasmOrTears is such a person: only that their perception of what the EU does may have been affected by the long-running Make The EU Look Bad campaign.)
So does the EU. MEPs are elected just as democratically as MPs (in the UK), Representatives/Senators (in the US), etc.
Magna Carta was about the balance of power between the king and the barons; commoners' interests come into it only incidentally.
The American Revolution is a slightly better case, but note that its "No taxation without representation!" battle-cry wouldn't be any sort of case against the EU because (1) everyone in EU countries does have respresentation, and (2) while for some countries EU membership is a net cost (at least if you ignore the benefits of free trade, free movement, etc.) that cost is a tiny fraction of those countries' total revenue base; e.g., the UK's net contribution is about £8B/year, which is a little over 1% of total UK taxes.