As a short answer, though, we're actually quite cheap for most customers. Major internet publishers use Zencoder for a few hundred dollars/month. Large-volume providers use us for less than the cost of a full-time engineer - and the alternative to Zencoder at large scale is a team, not a single engineer. Mission-critical encoding requires a lot of engineering and operations, even when starting from the excellent open-source libraries available.
Beyond that, we generally do things faster, more reliably, and at higher quality than "default" encoding systems, especially around the edges. That's what happens when you throw >10,000 hours of engineering at this problem. Again, get in touch if you want specifics.