A good question. In pre-EELV studies, NASA and the U.S. Air Force looked at LOX/methane. EELV resulted in the LOX/kerosene Atlas V and the LOX/hydrogen Delta IV.
At the 4th International Conference on Launcher Technology in 2002, Burkhardt et al. compared a reusable LOX/kerosene launch vehicle using the RD-180 type engine from the Atlas V with a LOX/methane vehicle using a possible engine of the same efficient staged combustion cycle:
The LOX/methane engine had about 3% higher specific impulse but that advantage was outweighed by the lower density of the liquid methane compared to kerosene.
LOX/kerosene was slightly better performing overall in terms of payload and expected to be lower cost to build and operate, the same result as the pre-EELV studies.
The reason LOX/hydrogen is comparable to or better than LOX/kerosene is that the specific impulse is much higher overcoming the even lower density problem. For the Space Shuttle the main engines operated from ground to orbit so the higher specific impulse of hydrogen at higher altitude was the reason for its use.
For a first stage that only operates to low altitud followed by a LOX/hydrogen second stage as in the Atlas and Delta, kerosene has comparable payload performance and may be lower cost because of vehicle size. For the Delta IV another advantage is commonality with the upper stage propellants.
Methane is not currently supplied at launch sites so a major facility investment would be needed.
Lack of long experience with operation is another negative for methane.
If the Raptor were to be used in space as in a Mars mission then the fact that both LOX and liquid methane are relatively easy to store in space compared to hydrogen or kerosene would be an advantage.