Exactly.
Returning to the OP, the whinging is well-justified in part even if it's done badly. Even some Trump supporters are capable of recognising that he won more because of a badly-designed system than anything else -- so how do you think Hillary Clinton's supporters, who are after all the plurality in this election, feel? Cheated, I should say.
More of them might have turned out, of course. But still, the fact that the US electoral system is so badly designed (essentially, it prefers states to the people who live in them) shouldn't be tolerated. One of these days, instead of shrugging our shoulders as political systems that made sense two-hundred odd years ago, but otherwise doing nothing, we might get around to updating them to reflect better the people they are meant to serve.
Again, the parallels with Brexit can be easily drawn. How many people here have expressed their anger at the recent court decision that, in essence, told them all that the referendum they voted in had no meaning unless Parliament endorsed the result? Even though I've pointed out that they should, morally, do so, it hasn't assuaged fears that the ruling will allow MPs to overturn the will of the people. But hey, that's how the system works, so why are you moaning (or, as some people have talked about, why are you planning to protest in the streets or riot? Heck, Nigel Farage plans to lead a huge march on the Supreme Court on the first day of the hearing there).
I would have thought the answer is obvious: because it's a bad system, badly designed, and badly implemented. In this case there was a possible fix, which is to have written the relevant act better so that the result would have been binding in law. Or, we could realise that in future referenda must be held according to set rules that make it clear what the outcome is and what its effect in law will be. You shouldn't really have had to put up with such a bad system, and why not complain about it.
And nor should those who lost on Tuesday, even though they were on the winning side in the popular vote.