As CrunchGear notes, the problem isn't that the Nook is using info Microsoft feels is protected by their patents, just that they are not paying licensing fees. Last year Microsoft and Amazon entered into a broad patent cross-licensing agreement and it covers the Kindle.
It is unknown at this point if Barnes & Noble is interested in entering into a similar agreement, but you'd think it wouldn't come to a lawsuit if the two companies were having productive discussions. B&N hasn't commented on the suit as of yet.
B&N is already on the ropes financially, as are just about all bricks and mortar bookstores. Borders is in Chapter 11 and closing about a third of its stores across the US. B&N's stock has tumbled from nearly $24 a year ago to $9.25 today on similar concerns. The Nook is the one bright spot since it has garnered around 20-22% of the ebook market.
How long do you think these suits against companies using Android will go on? Thus far, I haven't heard Microsoft losing. Rather it seems companies like Amazon, HTC and others enter into agreements to cover themselves.
Microsoft is going after the smartphone market hard with Windows Phone 7, but wouldn't it be ironic if they made more money off of Android licenses?