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Google is fickle when it comes to sitelinks. There's not a lot you can do to control them aside from telling them which pages NOT to show for certain URLs in Webmaster Tools. There's definitely a correlation between your highest-authority pages and pages that appear prominently on your site by default. The only thing you can really do to get site links is to prove to Google that you're a brand and that you appear more prominently in a search for something like your brand name. It's less a technical matter and more a matter of spreading the word about your brand. Links, shares, online mentions, and real-world awareness branding actions are all likely to help.

I have no evidence of this but maybe Google is taking into account your clickthrough rate. If people search "ProtonMail", and almost always go to the login page they might have bumped it up.