Why does Flink use Yarn?
Flink is not tied to YARN. It can also run on Apache Mesos and there are also users running it on Kubernetes. In the current version (Flink 1.4.1), there are a few things to consider when running Flink in Kubernetes (see this talk by Patrick Lucas).
The Flink community is also currently working on improving Flink's support for container setups. The effort is called FLIP-6 and will be included in the next release (Flink 1.5.0).