There has never been a Mac OS X virus in the wild, and only a few trojans. Your problem has nothing to do with malware.
I use Flash on Safari with ClickToFlash to control which content plays, and I have zero issues with it. Generally speaking, Flash is notorious for consuming system resources, raising temps and decreasing battery life. For Flash-related issues:
- Find your Flash version and make sure it's the latest version available. Never install or update Flash from a pop-up on a website. Always go to Adobe's site to get Flash or updates.
- Install ClickToFlash (Safari), Flashblock (Firefox) or FlashBlock (Chrome) to control which Flash content plays on websites.
- Install ClickToPlugin (Safari) to prevent Safari from launching plug-ins automatically, resulting in faster browsing, reduced fan usage, and increased battery life. It can also replace many plug-in-based media players with Safari’s native HTML5 media player.
- Try using the YouTube HTML5 Video Player to watch YouTube videos, when available. (May impact fullscreen viewing. See link for details.) Some have reported better performance with HTML5, while some have reported worse. Try it and find out what works best for you.