The main problem was that you couldn't sell your stuff, were forced to sell way below market price to Nazis [1] and countries wouldn't take you in [2] So many people didn't even have money because they couldn't sell at market prices or were murdered because they could not flee outside of Europe. Of those that could flee and sell their stuff, yes, those had to pay a lot of money to get away. But they were only able to get away legally after paying the "tax" and have a certificate.
The article makes it look like everything would have been fine if people could transfer money with a password in their head.
I just read on Wikipedia that the exit tax was 25% from $700k, later revised downwards to $200k. I'm assuming that's on total assets, not just unrealised gains.
Obviously not defending what had happened here, but that doesn't seem unreasonable in a time of war? Currently the US also levies an exit tax of around 25% on unrealised gains.
At the time it was also quite easy for wealthy people to evade taxes and not be prosecuted for it, for the better part of the 20th century.
I'm assuming, at the time, people had more pressing issues to deal with than their money...