Are trademarks as big of a hassle as software patents in the eyes of most Linux users. Surprisingly, no, as it is only designed to protect a brand and not code belonging to the community at large. Yet at the same time, I think many people fail to realize that it is trademarks that allow some of the most popular open source products to grow in a commercial sense, while still staying true to their brand identities. Ubuntu and Firefox come to mind, while other lesser known examples also exist.
Software patents on the other hand, translate into a problem where the community is often stuck trying to work around them even if the company that maintains the patent is not using any of the code for anything at all. While within their rights, it is quite annoying for a number of developers to have to work around.
While the folks who follow this article may believe that trademarks are more of a problem than a way for companies to use open source while protecting their investments, the fact of the matter is that trademarks are simply part of doing business in the world today. That and it has nothing to do with restricting the freedom to use the code that they might happen to be associated with. In the end, I see no problem with trademark usage myself.