While Amazon's service has a price advantage, there are some differences that could justify Zencoder's premium for some customers.
Amazon gives you a maximum of 4 encoding pipelines. These operate like queues. If you are processing many jobs simultaneously, and encoding multiple versions of each video, then those queues could start to build up. With Zencoder, all your jobs are processed in parallel, no matter how much you throw at it. In my experience, queue times with Zencoder have averaged <10 seconds.
For batch jobs, that aren't sensitive to encoding times Amazon's queues shouldn't be a problem (ex - a media company encoding a huge library into a bunch of different formats). Business video services or online video platforms may want to optimize around keeping queue times low to get client videos out quickly.
Zencoder also seems to be working on premium services like closed captioning (an FCC rule says that programming that is shown on TV must have closed captioning when it is shown on the web), live streaming, and packaging HLS streams. Finally, Zencoder supports formats like ProRes 422, that Amazon may not (I haven't seen a list of input formats yet). Zencoder also has great support and a great API.
I'm a Zencoder customer and don't have any vested interest in the company. In fact, I'll be taking a look at the service to see if it meets our needs. I just wanted to highlight that if you are making a decision around transcoding, you need to define your requirements, understand the trade offs, and test the different options.