Malware and viruses like to use holes in Flash and Java to infect your PC. In some cases, they come through advertisements from legitimate sites.
I know it can be annoying to click on those pop-ups when they come up to update Java, Flash, etc. and it seems like they are trying to update everyday. Ninite has a tool in which you can update all those programs at once.
You can run this tool as often as you would like and it will check for updates and install them if available. For most people, I would recommend using this tool once or twice a month. Remember to also keep up to date with your Windows Updates as well.
Enjoy! – Justin