It isn't clear to me that they are using trademark law to silence critics. IANAL, but based on my understanding of nominative use, I do not see how this use of the logo qualifies. Let's look at the list of general criteria for nominative use in the Wikipedia article linked in the OP:

1. The product or service cannot be readily identified without using the trademark (e.g. trademark is descriptive of a person, place, or product attribute).

2. The user only uses as much of the mark as is necessary for the identification (e.g. the words but not the font or symbol).

3. The user does nothing to suggest sponsorship or endorsement by the trademark holder. This applies even if the nominative use is commercial, and the same test applies for metatags.

The use of the logo in this case is not necessary to identify Ubuntu. If the site in question had just used the name "FixUbuntu", it is doubtful Ubuntu would have cared. But not only do they have this vaguely official-sounding domain name, they also had the Ubuntu logo as the most prominent art on the page and did nothing to disclaim the association.

In response to the complaint, the site has dropped the logo and has also added a disclaimer. I'm betting Ubuntu will be OK with this.

I sympathize with better default privacy settings too, however you must note that they didn't ask you to remove all references to Ubuntu: They only ask you to remove the logo and the domain name. You can understand they need to make it clear in the cinsumer's mind what belongs to the official sphere of Ubuntu and what doesn't. Also, before saying they're using it against privacy, we should check whether they've asked to take down similar domains with no correlation to criticism or privacy, and they answer is probably yes.

As kcorbitt says, the trademark law requires ongoing enforcement or the owner will lose the legitimity. Have you checked whether they'd let you keep talking about Ubuntu? IANAL, but wouldn't it be correct to keep a website named "Fix Ubuntu" in a domain name such as privacywatch.com? This way they keep the integrity of the brand for the consumers and you stay in the ecosystem.

While I sympathize with your situation my understanding of trademark law is that it's a sort of "use it or lose it" proposition. If they can't demonstrate that they're making an effort to police their trademark then it can become generic and they lose all exclusive rights to it. I think the best solution here would be for you to choose another domain name.

http://cyber.law.harvard.edu/metaschool/fisher/domain/tm.htm...

Sensationalist BS. Canonical isn't trying to silence anyone. They have _the same information_ on AskUbuntu.com, a site directly supported by paid Canonical employees.

http://askubuntu.com/questions/192269/how-can-i-remove-amazo...

None of these settings are relevant to 12.04, are they?