LOX/LH2 motors have a good enough Isp figure that they can take the hit in performance -- the Vulcain 2 runs between about 360 at sea level and 420-odd in vacuum, comfortably outperforming vacuum-specific kerosene/LOX designs at all altitudes. The SpaceX Merlins are actually quite poor performers for kerosene/LOX but there may be other trade-offs in terms of construction costs and reusability. They can certainly do the job of getting modest amounts of materiel into orbit.
As for the Raptor engine I'll be interested to see where they go with it. Other people have tried methane/LOX in the past but reported problems. I've heard there is a fuel decomposition problem resulting in coking of the pumps as well as sulphur impurities in the methane causing problems too. What puzzles me is the mention of using a partially-cryogenic fuel mix as an interplanetary engine; LOX is not storable over any sort of a timescale even in space and even methane would require active refrigeration to stay liquid for weeks or months on end during a transfer orbit to, say, Mars.