There are many reasons for security flaws in Windows OS. Few of them are below.

1. Original design of Windows didnot take access permissions seriously. FAT32 filesystem severely lacked ACLs unlike UNIX like OS which had robust filesystem access control from the onset. This caused any virus to access any file including system files and MBR without much effort and corrupt the whole system within seconds.
2. Too many third party applications and continuing support for legacy applications which were poorly written became target of hackers. There was severe lack of quality control / certification of Windows programs which jeopardized user security and system stability.
3. Windows being a commercial OS, many application developers keep developing feature rich but sub standard programs without paying much attention to security and stability of the program jeopardizing the security of the user and the system.
4. Many auto start programs and many services started by Windows by default are easy targets for viruses and hackers as it does not require user intervention to st...