Apple disables Flash Player by default in Safari 10. If Safari is prompting you to Trust (allow) Flash Player plug-in on a specific page it would indicate the page contains some Flash content. You're free to allow or not allow. If the page doesn't display correctly you can go to Safari > Preferences > Security and modify the plugin settings (Enable Adobe Flash Player for Safari)
Thank you. I'm aware of all that.
What I'm wondering is whether a site like PayPal or MacRumors would have a legitimate reason for using Flash.
Is Flash used for things other than video and games?
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You would need to contact PayPal and MacRumors to find out for sure. A search of "does PayPal use Flash Player" returned the following:
Yes, Flash is used for things other than video and games. Many custom apps (e.g. AIR, Flex) use Flash Player.
I've experience this as well. In the past couple of months, it seems I get this prompt ten times a day from all sorts of websites that seem to not use Flash at all anyway. Maybe they do, but like you say, I don't see any adverse effects at all from disallowing it.