John Timmer writes for Ars Technica (article link): "At the same time that Microsoft was pushing for the adoption of an XML-based file format for documents, it had a patent pending that would cover most uses of XML for word processing files."
One of the reader, Doornail commented on the issue in reply to the Ars Technica article saying: "Everyone at the USPTO needs to be neutered, fired, the buildings burnt to the ground and the soil salted. This is beyond paint-chip munching stupid."
Why is the anger directed at USPTO and not at Microsoft? Well, the answer is that it is the responsibility of USPTO to examine patent applications. Microsoft's actions are designed to protect Microsoft's interests.
One argument is that software patents are not good for anyone, except for squatters. For the hundreds of thousands of patents that Microsoft owns, there could be five held by a squatter that would make it impossible (or prohibitively expensive) to implement an efficient solution.
For more on software patents, please read this extensive article on Wikipedia: Software patent debate
For a completely(?) unrelated rant, please continue reading:
Microsoft is a for-profit business entity that needs to protect itself, by any means possible. When Microsoft tried to embrace, extend, and ... PDF with built-in capabilities in Office 11 (officially 2007 Microsoft Office System according to Wikipedia), Adobe cried foul. Adobe wanted to make sure that a third-party vendor could not dictate the implementation of the portable document format. Of course, Microsoft did not see it that way with Brian Jones writing a blog post calling Adobe PDF "actually not open". As a comment to the Brian Jones blog post notes from an official Adobe document: "[...] Adobe’s intention is to maintain the integrity ofthe Portable Document Format standard. [...]" (page seven in the document in the link to Adobe's document, which is of course formatted in PDF).