I agree with you somewhat. There seems to be a divide between the cases of the text. Since Microsoft's framework is named in all upper-case.. it seems to be the convention for .NET framework related apps/companies. If a company was named "Orange.net," I wouldn't think they were related to MS or .NET.
There are a lot of companies and products that use this name... I'm sure you've researched it a bit, I can think of about 5 off the top of my head. My guess is as long as you aren't a threat to Microsoft's income.. you'll be just fine.
I'd consult with a lawyer first, but I think you're good to go. There are many apps and websites that have ".net" in their name, and the .net domain predates Microsoft's framework by quite a bit.