I have hope that SpaceX BFR will break past the sonic boom problem by doing the zoomy stuff outside the sound transmitting parts of the atmosphere.
The thought of making a colander out of our ozone and ionosphere sends shudders down my spine.
But yeah, it probably isn't ideal for the atmosphere.
Although I suspect that long-term, if you're synthesizing your fuel, you're better off using hydrogen instead of methane. Structural mass is generally higher if you use hydrogen, but there is a performance boost especially at higher velocities. And you avoid the inevitable energy loss from the Sabatier Reaction. And generally better for the climate than methane, particularly if you're running fuel-rich.
The total size of the launch market today is infinitesimal (~100 launches per year and vast majority less than a tenth the payload capacity of BFR). But BFR is being built to change that by orders of magnitude. Long-haul point-to-point transport of people means potentially hundreds of thousands to millions of flights per year. Long road to get there, though, and the primary obstacle may just be the incredible airline safety record (to make it close, you probably need to include lifetime saved by making the trips shorter).
But, like I said, premature and superfluous, even though we should still do our accounting carefully, and not rely on "OMG methane!" as the guiding principle of our thinking.
It may be tough to have a reusable hydrolox rocket that's efficient from a total cost of ownership perspective.