The main reason is support, usability and control. First, lets clarify that FFMPEG is an encoder, QuickTime Pro is a video utility that happens to include multiple encoders and Final Cut Pro is a non-linear editor and has nothing to do with encoders other than the fact it can output to an encoder (generally QuickTime I believe).
For big budget commercial projects, the emphasis is going to be on having the highest possible quality encoding which often will involve manual review of the content and tweaking the way things are encoded to minimize artifacts and maximize the quality. Commercial encoders or even proprietary ones used internally by encoding houses have far more control, support and development than ffmpeg. It's great for a free tool, but it isn't a high end commercial product.
For smaller commercial projects, you may find some users, but most often people use the encoders that come with their NLEs at that level (such as QuickTime Pro or Adobe Media Encoder). The main reason at that level is convenience since they are tied directly in to the NLEs and are easy to configure and behave well with good quality results.
I can't guarantee that there aren't any production chains that use FFMPEG or a modified form of it, but in general, it is worth simply pointing out that not all encoders are created equally and while ffmpeg does very, very well for being free, it isn't the best option in all cases all the time, even if for business reasons rather than technical ones.