"the intelligence guys will emerge promptly at your doorstep" - for the US, I'm emotionally inclined to agree with you.
ProtonMail was developed in Geneva, where I grew up. It was a spin-off from people who worked at CERN, like the World Wide Web itself.
Geneva is also a United Nations base, and many other NGOs are headquartered/have offices in the area for that reason (the Red Cross, WWF, Amnesty, Greenpeace). There's a lot of local community support for the operators of ProtonMail.
Switzerland is not EU, although it is Schengen. International incidents occur all the time, such as the time I forgot to take my passport when going to school (my parents live in France, but I went to the International School of Geneva in Switzerland). Because people don't need a visa to cross the border, it would be easy for an intimidated web developer to flee the country. Attempting to get an extradition would then require an arrest warrant, which would require a criminal case to be brought against that person in absentia. Although intelligence services can try to threaten ProtonMail (and probably already have), there are a lot of options available in that area to keep individual staff safe.