From wikipedia (sorry): "Trademark law is designed to fulfill the public policy objective of consumer protection, by preventing the public from being misled as to the origin or quality of a product or service. By identifying the commercial source of products and services, trademarks facilitate identification of products and services which meet the expectations of consumers as to quality and other characteristics."
Trademarks exist to protect consumers, not the "owning" companies. In case of open source projects, this does not work so well and there are problems you have mentioned in your reply.