Did nobody run a simple Google search before picking the name?
Also, this project
https://github.com/freifunk-gluon/gluon
predates GluonHQ by several years.
Now, if Intel were to go after the Atom Text editor, we would agree that'd be pretty silly, no? Obviously they wouldn't, because there is no confusion. Now, if AMD were to start selling ATOMe processors, I'd also agree that Intel would have a reasonable complaint.
There is no reasonable confusion (for the target markets) between this gluon project, gluonhq, and the router gluon project (linked to above).
Trademarks are scoped by product category.
Trademark isn't about inventing new words. It's about one party at a time being able to use the same word as a brand within the same field. It's one of the few aspects of IP law that actually makes good sense.
Moreover, if you allow your trademark to become "public vocabulary", then you lose it. "Aspirin" used to be a Bayer trademark. "Xerox" and "Kleenex" have to work really hard to discourage writers from using those brand names in a generic way, etc.
That may be how it shakes out practically, but it's important to remember the motivation behind trademarks isn't to protect companies, it's to protect consumers from the confusion that ensues when two different entities use the same name. That may seem like a trivial distinction, but it can be important when evaluating a situation based on the spirit of the law. In this case, while the commercial entity may not want an open source project using the same name, that reuse is unlikely to cause confusion for consumers. However the merits of the case are largely irrelevant since a C&D on the part of the commercial entity would likely force a name change long before the courts were ever involved.
while http://gluonhq.com/ does not.
In fact, for me, it's the last link on the first page. The rest are all about physics.
Since they are clearly so tiny any claim to trademark might be problematic. Furthermore, the domain is different. They can't assert computers as a domain (gluon gun from Quake if I remember correctly). It is used as a sort of umbrella name for a lot of different products they have but none of them is a programming language.
The username is about the least interesting part of the url. What persists between forks? What happens if you reupload the project to an alternative host? What's it look like on-disk? What's it called in all the docs?
Not "Marwes's gluon", not "Marwes's github hosted gluon", just "gluon".
In context, the URL is hosting minutiae, not part of the mark.