It's about protecting your users, and protecting your project.
Take a large, reputable open source project like Audacity. If some scammer comes along and bundles their own version of Audacity with some spyware and tries to distribute it under the Audacity name, this is damaging to both users and the reputation of the software. Audacity's defense against people like this is their trademark. Nobody will confuse real "Audacity" with any ripoff, because nobody else can use the name.
This also protects the developers, who have worked hard to produce great software, and who deserve to have it recognized as something special on their resumes/CVs. Preserving the reputation (ie. name) of your software project helps ensure their contributions to the project aren't devalued.
Lastly, the Mozilla example in the article can easily be countered by the infamous OpenSSL/Debian fiasco, where a Debian packager incorrectly patched OpenSSL and created a vulnerability. This was certainly damaging for OpenSSL's reputation, even though it wasn't their fault. If Ubuntu decides to patch Firefox and introduces bugs, it's Firefox (NOT Ubuntu) who looks bad to users. IMO this is good justification for exercising ownership of your trademark.