You're right on progression and Gewerbesteuer deduction. Nevertheless I pay tax rate "Höchststeuersatz" at 45%. Add "Solidarzuschlag" and you end up very close to 50%.
Yeah this is not really how you do the math (and your salary should count as expense for the Gewerbesteuer no?)
You should calculate the end % of tax. The 45% is the marginal rate. Also the solidarity tax has a ceiling
(And not everything is charged the full VAT rate)
And in the end, that number doesn't mean much? Switzerland for example had much lower tax, but your cost of life shot up. Some other places your income tax might be lower but sales taxes are higher.
It's all relative
Edit, as an example for 200kEUR in Berlin your tax will be ~ 43% (Cat I) - for 1MEUR/yr you're paying 46%
(this is not so much about Berlin or Germany - the math is the same everywhere - it's about people thinking that the rate means they pay that % of their salary)
But the 45 % is only paid for income above 277 T€ (or twice that much if you're married)? I mean, it's a lot but if you alone are in that tax bracket you should be able to afford housing in Germany and Berlin, that puts you somewhere in the top 0.5 % of all families, not even accounting for your partners income.