And how about if the vote had been phrased as "do you wish to remain in the EU", with a 2/3rd requirement to meet the bar, meaning 1/3rd was sufficient to trigger Brexit? Would that have seemed fair?
Democracy evolved as a shortcut to avoid fights. Just count and you got a rough idea of which side has the most people and thus, is more likely to win if it came down to it. Once you start tipping the threshold in order to bias things towards your preferred decisions, you increase the risk of the losing side thinking ... wait a minute. We could win this. That's far worse than any other outcome.
The EU and its supporters constantly warp the system to try and make it hard for people to leave, hard for the people to reject their policies. It is fundamentally undemocratic.