In Falcon 9's case, and totally from memory and probably incorrect and very approximate, we've had 4 launches, each has had 9 Merlin C engines on the first stage, the first stage burn time is 170s or about 3 minutes. There have been two failures - a non destructive engine shutdown on the previous ISS mission on the pad at T-very_little, and the rather more messy rapid disassembly failure of something near the engine or the engine itself on the most recent launch.
So, for this first stage engine the MTBF (remember this is all a bit silly and inaccurate and just for ballpark comparisons with the airline industry) the MTBF has been:
9(engines/launch)4(launches)0.05(3 min burns in hours)*0.5(2 failures) = 0.9, i.e. a MTBF of 55 minutes for Merlin 1C lower stage, vs most regulators requiring mtbf > 100000 hours on commercial jet airliner engines.
So there's a bit of a way to go yet!
I don't know if it makes sense to normalize for thrust or not, but it seems like thrust should be included somehow.
It doesn't make sense to normalize for thrust here. This is just failure rate. There's nothing wrong with having a comparatively high failure rate when the sample size is several orders of magnitude smaller: the statistical significance is just weaker; we acknowledge that and move on.
http://ntrs.nasa.gov/archive/nasa/casi.ntrs.nasa.gov/1993001...
Incidentally, I went searching for airliner engine MTBF statistics and your comment was already near the top of Google's results.
Edit: erroneously said five million flights per year because I was looking at 2012 statistics for only the first six months. of the year. Oops.