The message appears when the site from which you downloaded has been flagged for distributing malware. It doesn't necessarily mean THAT particular PDF contains malware, although it's possible.

More about managing this feature here: How does built-in Phishing and Malware Protection work?

As I understand it, all pdf's from every ISP (Comcast in my case) will be flagged. Somehow that doesn't make sense to me.

Do you mean they are email attachments stored on Comcast mail servers that you are opening from a message?

Is the warning displayed in the Downloads panel (see attached screenshot), or in a different way?

What about PDFs from other sites, such as this one on my site: http://www.jeffersonscher.com/gm/Google-Hit-Hider-by-Domain_About_v160.pdf

The PDF's that have the error message (This file contains a virus or malware) are PDF attachments on a Comcast.net email.

The PDF link you sent opened normally. However I saved it and sent it to myself at my Comcast email and it was flagged (This file contains a virus or malware).

It appears to be a Comcast problem.

This may also be interesting. I have 2 computers, a MacBook Air (MBA) running FireFox 48.0. and an iMac running 49.0.1.

The problem is only on the iMac, the MBA can open the same PDF's

Firefox uses a list from Google's SafeBrowsing project, so your two machines may have different versions of the list. Not sure which is the most up-to-date... I guess we'll see as they eventually download the next version of the list.

Anyway, this is why Firefox now has a right-click override on those warnings, because when a large provider is flagged, there are many false positives.