Again, I am not arguing that suborbital flights for transport will be practical. Ever. And certainly not in the next few decades. But debunk it with real facts and numbers, not with scary what ifs. Having said that the following areas are what ifs that are hard to put real numbers on.
The noise problem is real, and is probably the only part of this that can't really be numerically evaluated. Even if it could be proved harmless to humans and the environment, there are sufficient people who are offended by the noise, by the idea of spaceflight or by Musk that is just won't be allowed. I wouldn't even try to attack it. Just go out to sea or into truly unpopulated areas and deal with whatever problems that causes.
Economic attacks are also difficult. Almost all travel is not necessary. It is done for emotional reasons. This is particularly true for first class seats. There is some minor time savings from being in these seats, but there are enough people who are willing to pay for some combination of a few minutes quicker deboarding, a posh experience, and the bragging rights of being there that they are almost always sold out. Guesses about what a suborbital flight seat will cost are just that - guesses. I am sure that the masses won't be able to afford them. But I wouldn't venture to guess how many zeros you need in your income or your fortune before people are willing to pay for them. The space tourism thing isn't mature enough to provide any real data, but they seem to be selling a fair number of seats in the million dollars to ten million dollar range. SpaceX has an aspirational goal of getting cost to orbit down by three orders of magnitude. One can imagine that if they only get it down by a factor of ten the number of buyers will skyrocket. If they get it down by a factor of one hundred (unlikely, but doesn't seem totally impossible) you are starting to be in the same order of magnitude as high end first class travel currently.
Safety is a real issue. It has both an emotional and regulatory component. Rocket flights will be distinctively less safe than airplanes forever, and the difference will be huge in the near future. But safety is a weird thing. I know many people who won't travel by air because of safety concerns. These same people travel by automobile or train, which is demonstrably more dangerous. Even for properly understood safety risks people have different risk tolerance. I am one of those that would have gladly accepted a trip even though the chances of getting back alive were only about 97%. Others feel very differently. The regulatory side is the real issue. At least here in the US safety has become paramount, and I am really surprised that the space tourism flights that have occurred have been allowed. Perhaps being offshore even further, outside the legal jurisdiction of the US would solve more than the noise issues. But there would still be problems selling tickets in the US and transporting people to the from a US location to the spaceport.