It is, although you have to read between the lines (and perhaps know a bit of Schneier's previous writings): when Schneier talks about locked down devices, it's helpful to know that previously he has talked about open source as necessary for good security (http://www.schneier.com/crypto-gram-9909.html), therefore locked down systems where you can't get the source (or run your own software) cannot be fully vetted for trustworthiness. This applies on two counts: if you cannot get source, you have to have faith in the competence of those providing the software, as well as trust that the motives of those offering it are in your best interest. With open source software, you don't have to make either one of these (dangerous) assumptions.
Even if the software was free, Microsoft could still spy on you. (I'm planning on writing a much more detailed response about how this relates to free software and SaaS later today; I'm stuck at work for now.)
Skype is "free software." I take it you mean /open source/ software?
Frankly it is because there is NO open source software in the VoIP/IM/etc space that is worth five minutes of your time, let alone full usage of.
Every time this point comes up the OSS apologists start naming some convoluted solution involving stringing five different software packages (and a SIP provider!) together to get even then a barely workable solution.
In general this is one of the least competitive sectors that exists. Right now we have Google+ and Skype, and even Google+ barely implements 1/8th of Skype's feature set.
The term "open source" was coined to sell free software to business/the masses, ignoring the core of RMS' philosophy (with which not everyone agreed). The terms are different.
