I have received e-mails from Protonmail users that even when I whitelisted them on my local e-mail client (Outlook 2016) they were "junked" at the server level.  I doubt many folks monitor their e-mail address junk@yourhostname which is separate from your junk folder you set up on your e-mail client.    

I do monitor the server junk account and this is the first time I recall finding a legitimate messages in junk which I rarely scan (most are in foreign languages) They were both from ProtonMail accounts.

In researching the issue this seems to be a common problem with the free account.  For the paid accounts you are assigned a "cleaner" IP.

Here are some posts I found:
"ProtonMail seems to be the choice of mail service for most new spammers on my forum. It was a surprise when I noticed that most of the new accounts were using Protonmail service for emails.

"This is actually a big problem and has the potential to lead to Protonmail being blacklisted across a variety of sites if admin's start banning @Protonmail domains.

"I actually worry that this might eventually affect paying customers as well, as businesses limit/ban Protonmail domains for abuse."

Another poster said he had sent a lot of business mail using Protonmail and found many were not receiving it.

While ProtonMail servers are exclusively located in Switzerland, and encrypted, the U.S. still has jurisdiction over Protonmail.com via VeriSign but not Protonmail.ch in China.

Neither is on major blacklist's that I could find but they are "junked" at the server level by some ISPs it seems clear.

Further, the encryption only works seamlessly if both sender and receiver use Protonmail.  

When you send a message to an email recipient who does not use ProtonMail, you get the option to encrypt it with a password. The recipient can pick up the message using the ProtonMail web interface but has to receive the password another way - unencrypted.