With Bitcoin you are the boss! That not only means you are in charge, but that you must work. Bitcoin security is no better than your security. If used correctly it is miles above the bank's security system. However if you do not protect your private key then no other methods matter.  

I don't know how this happened to you, but someone must have gotten that key. Consider who else has access to your computer. Think about where you store your private key. This breach may not involve malware at all. Also, Think about a more secure OS like Linux.

Sorry to hear about your loss.