Safari 10, due later this year, is to have plugins such as Flash, Java, Silverlight, and QuickTime disabled, while Apple shifts the focus of the browser to HTML5 content.
If your site has both Flash and HTML5, Safari will always show users HTML5 content, instead of Flash, or other plugin content.
Apple is encouraging web developers to check how a site might be impacted by the changes, and ensure sites are compliant.
To avoid making your users have to explicitly activate a plug-in on your website, you should try to implement features using technologies built into the web platform. You can use HTML5 <audio>, <video>, the Audio Context API, and Media Source Extensions to implement robust, secure, customized media players.
It's really worthwhile reading the whole blog post about the recommendations for developers.