Penance is cheaper than flash heal, and has better HpM.
Additionally, it has a good synergy with Borrowed Time : one of the best sequence to use the buff is to cast penance, PoM, and still use it for a big slow heal (greater heal or PoH). In particular, it belongs to a very good emergency sequence : cast PW:S, then a hasted Penance if needed, and you most likely saved someone's life. You can follow with a (greater or regular) heal, on that target if needed. Or use POM, if the cd is free. Or go back to other raid healing duties.