This had probably started way back when Microsoft created ASP.NET Web API library, at least that's when I remember it if I am not mistaken. Anyway, since then, its HTTP packages started depending on Newtonsoft.Json library for data (de)serialization to and from JSON.
Why would a company as large as Microsoft would add a dependency on an open source library? I find it strange even if they were going to go fully open source with .NET back then because it has been the only non-Microsoft library used as a dependency, as far as I know.
As a bonus question, does James Newton-King get any financial support from Microsoft?