Thank you for your replies guys.
I agree rooding the device decreases the overall secruity of the device.
On the other hand, rooting the device gives access to the apps that give you control over the system and data on it. For example as Elzbach wrote, with the app XPrivacy I can control what apps have access to my personal information.
Now - without root - when I instal a new keyboard or launcher with widgets, I'm warned that these apps can have access to my personal information and can use them malicously. For me that means, that even without root using normal apps I can get big security risk when using some apps from play store.
Do you build the custom android version by yourself from the source or use builds provided on this forum or modaco or use another way?
XPrivacy, and apps like them introduce additional security concerns of their own. Android is not designed to work the way they force it too, introducing many new unknowns.
New keyboard, launchers introduce an infinitely smaller risk than any root app, and unlike with root apps you are warned and privileges are handled by an established well tested permission system. Comparing the two is completely silly.
Any developer, in a matter of minutes, put together a root app requesting 0 permissions, that can gain permissions or otherwise use APIs requiring permissions at runtime without declaring them, and disable or work around any "security" any XPrivacy type app claims to provide. Once rooted, apps like XPrivacy provide a complete false sense of security. Given you need root to use them... they provide no real security at all.
A completely valid scenario (one we have seen in the wild): An app with 0 permissions, but the ability to use su could download and dynamically execute new code to perform the malicious activities. IE Google bouncer, and any anti virus software would be @#$@ out of luck on that one. All because a user decided to completely break the basic security model, by installing su.
The only customized version of Android I use, is a customized emulator I use for analysis, and that only used when I suspect something could damage an actual test device.
I do not mess with customized versions of Android on real hardware, I only build when testing patches I plan to push to the AOSP gerrit for review.