Permanently accepting a new root CA is a decision that really ought to
involve deliberate human intervention, and I wouldn't recommend that you add
this to your application.  However, if an untrusted root CA should not
prevent the use of https in your application, you may want to consider
creating a custom implementation of the System.Net.ICertificatePolicy
interface for use as the System.Net.ServicePointManager.CertificatePolicy.
(Taken
together, the MSDN topics for the ICertificatePolicy interface and the
CertificatePolicy property form a sample of the technique.)

Even this more limited approach is potentially quite dangerous, and I
wouldn't recommend it, but it does pose less overall risk than blindly
trusting an unknown CA...