For the time being their interest are very much aligned with the EU (and logically so, from a geographical and economic standpoint), but Switzerland also has a history of happily changing sides when their "neutrality" or their financial interests are at stake.
Their historical dependency on finance (and their shady practices), combined with a high dependence on US trade, and high financial investments in the US make them particularly vulnerable to economical and financial blackmailing by the US. For a case-in-point, see the particularly weak response (or "diplomatic" response, staying charitable..) of Karin Keller-Sutter to the Trump developments, in a bid to hopefully avoid tariffs.
Therefore, companies obeying Swiss laws simply do not offer the same "privacy" guarantee as companies obeying EU law.
Secondarily, putting your trust in a company who's CEO openly supports the Republican party is, in the current context, very questionable. No matter the Proton PR denials and clean-up attempts after the facts.