The concern isn't necessarily about if Microsoft looks at the data, but more about what they do with it. Microsoft was one of the first companies to join the PRISM program, and the people that are against PRISM are the people that are against this. The thing that scares us is just the lack of privacy and the future implications of companies/the Government having this data. I don't want this to turn into a debate on privacy and the NSA, I just want it to be clear where the concern is coming from.
Also, there could be nothing to worry about. However, considering the NSA revelations, especially PRISM, I think this being an issue is very plausible.