Furthermore, Microsoft has universal access to Windows machines which connect to Microsoft servers to download patches. The government can argue with risk to national security and force Microsoft to let them use that update mechanism to spread their malware.
- Backdoors can be discovered; I'd assume it is less likely to be detected if you use it less.
- Esoteric network configurations may make the 'normal' backdoor inaccessable
- Securing their own systems
- Deniability - if an attack in progress is discovered, it's better for the NSA et. al that it looks like a bug being exploited by an unknown third party than a deliberate backdoor (though I suspect any backdoors, should they exist, are designed to look accidental).
Edit: typo fixed and clarification