I do not believe that muttering, in and of itself, is rude. However, it can be very annoying and (depending on the content of said muttering) it can come off as passive aggressive.
OP, you state that you aren't muttering to gain attention or get people to help you, but you have to recognize that there are a fair number of people who do mutter to that end. It's unfortunate, but you do run the risk of being lumped in with that.
On the other hand, I find myself "reasoning with" my computer, spreadsheets, or various kitchen appliances an awful lot. I think the best thing to do is follow Yvaine's advice and speak up in a cheery voice.