Recently some work was done with the GNOME logo and it was clear that the GNOME logo artists had chosen a non-free font—Trebuchet MS—for the text. The same critique applies to all of what were once known as the Microsoft “Core Fonts”. Microsoft no longer distributes these fonts but others have distributed copies under their license which allows verbatim non-commercial reproduction and distribution.
Trebuchet can be redistributed so long as one redistributes it in its CAB file (there is a free software program to extract the fonts from the CAB file). This is not a reason why the Trebuchet MS font is non-free.
I can see two reasons why the Trebuchet MS font is non-free: it cannot be redistributed for profit (section 1 of the EULA) and the font cannot be modified to suit one’s needs (derivative works other than subsetting for embedding in documents is prohibited in section 2).
Free software doesn’t discriminate against businesses; for-profit distribution must be allowed. Changing the software must also be allowed; you must be given permission to correct or improve the font (whether as part of business activity or not). If the glyphs you need to write in your language aren’t there, too bad. You are prohibited from adding additional glyphs. Hence the Trebuchet MS font is not free software because it denies the user the redistribution and modification freedoms the user deserves.
Should a free software OS (such as GNU) choose a non-free font for its logo? I don’t think so because this would encourage people to install the non-free font, and it’s not good to encourage people to take on the aforementioned shackles of non-free software.