I don't know if any of the major carriers still try that or not. Some of the minor ones still do.
It's been challenged in court, and whenever it has, it hasn't stood up and carriers have removed the clause - it's an unconscionable contract as I understood the explanation.
For us non-lawyers -
Unconscionability - Wikipedia, the free encyclopedia
Carriers hate it for all of the obvious reasons - potential support issues, removing bloatware, etc etc etc.
Carriers are allowed to not honor your warranty if you root - that's really about it.
FWIW - Sprint now honors warranties on rooted phones and lets you remove some/all bloatware without root (the number one reason to root). It's a very enlightened policy, imo.
In any case, AndroidForums.com comes down on the side of this being your phone, so granting admin access (root access in our world) is AOK here.
There are many valid reasons to root and I've no doubt that will apply to the Nexus for a good many here.