Sure, Switzerland is very much European, but they're not in the EU. Romanian taxpayers are now contributing more to ProtonMail than Swiss taxpayers are.
This would be very much like the US government subsidizing a Canadian software company, on the grounds that 40% of their users are American plus some of their developers live in Vermont and Kentucky.
But, well, at least it goes to the good guys! So yay ProtonMail, I guess!
EDIT: I stand corrected, please do read some of the very insightful replies people posted. Thanks everyone!