Some GTFS license agreements limit how the the agency logo may be used in 3rd party services. The agencies reserve their logo as a way of marking agency-provided/official information.
I believe that both TriMet and BART have included this in their license agreements. I have not looked at other license agreements.
All trademarks, service marks and trade names ("Trademarks") of TriMet used herein (including, but not limited to, TRIMET, MAX, TRANSIT TRACKER, THE NEXT BIG THING DOWNTOWN and QUICK DROP, the slogan "SEE WHERE IT TAKES YOU" and the TriMet logos (see below)) are trademarks or registered trademarks of TriMet and may not be used in any manner that is likely to cause confusion, or in any manner that disparages or discredits TriMet. The TriMet trademarks may not be used in connection with the products or services of others, except for the use of a text link or a TriMet web logo to link to this site, in accordance with these Terms and TriMet's linking policy. All other trademarks not owned by TriMet that appear on this Site are the property of their respective owners.
BART (
http://bart.gov/dev/schedules/license.htm):
BART trademarks and copyrighted materials, including any confusingly similar variants, may not be used in association with Data.