I have an app that gives option to install CA cert and it gets stored in the user tab of Trusted Credentials and it works as expected.
FYI
Lookout Mobile has blogged about this due to the DigiNotar events, and provided some pretty good (read: lengthy) instructions which you can find here.
The gist of it is that you need to pull /system/etc/security/cacerts.bks and then remove the CAs from the store, then push the store back to the device and reboot. Their instructions require that you have Bouncy Castle (for decrypting the store), root access, and a working adb connection. I'm not sure if this applies to all versions of Android or not, but my guess would be that the location of the CA store hasn't changed in quite some time (if ever).