Java/flashplayer a problem with hacking and malware!

I read in Computeractive recently that Java and Adobe flashplayer can cause problems with malware and wonder if this is slowing my computer. I have done a malware scan. If so what can I safely use for the bbc iplayer and so on to be shown as Iunderstood this software was needed?

Thank you,

Java/flashplayer a problem with hacking and malware!