Fair question. What you get is scalability (Softlayer is explicitly for low-volume transcoding), an API (Softlayer might have one, though it's not documented at the above link), a lower error rate, higher visual quality, better compression, more options, and hands-on customer support. Not everyone needs these things, but many people do.
I would think along the same lines. Then recently I was doing contract work that included ability to upload and preview video files. My client had a very average vps and was not willing to spend much on having me install/test a bunch of packages to get video conversion going.
Bring in zencoder and I had video uploads working for him in a couple hours.
(Granted, I think someone who knows their stuff when it comes to ffmpeg etc. could very well do this in two hours without zencoder, I think. Nonetheless, this is one use case.)
I'm using Zencoder on a new project, and I've been deeply impressed at both the ease of getting started, and the quality of the tech support. Their API builder lets me fill out a form, and it automatically displays the HTTP headers and the necesary JSON.
Even if I didn't already have a Softlayer server, it seems like it'd be cheaper to get one of those then hire Zencoder for many cases.