Air particles would be moved out of the way as the new body is being constructed.
I spent a long time, and I do mean a LONG time thinking this over and reviewing information in the Star Trek: The Next Generation Writers' Technical Manual, Fourth Season Edition. And I keep coming back to the points I've brought up in another question. While that provides support, it's not a full answer. I'm going to include some of that answer here as explanation.
I'm going to my source for this, one I've cited here before, the Star Trek: The Next Generation Writers' Technical Manual, Fourth Season Edition. This was sent to me directly, in a pitch package by the ST:TNG Script Supervisor Lolita Fatjo, when I was invited in to pitch story ideas to the producers. This is one of the Writers' Guides sent to those who would be writing for the show and, in some ways, goes beyond canon because it defines canon. In other words, it tells the writers what they can and cannot do on screen.
On page 28, under The Transporter - Once and for All:
... The stream of molecules read by the pads is sent to the Pattern Buffer, a large cylindrical tank surrounded by superconducting electromagnetic coils. It is here that the object to be transported is stored momentarily before actual beaming away from the ship (or even within the ship). It is the Pattern Buffer and its associated subsystems that have been improved the most in the last half-century. While the actual molecules of an object are held in a spinning magnetic suspension (eight minutes before degradation), the construction sequence of the object can be read, recorded in computer memory (in some cases), and reproduced. There are limits to the complexity of the object, however, and this is where the potential "miracle" machine still eludes.
The Transporter cannot produce working duplicate copies of living tissue or organ systems.
The reason for this is that routine transport involves handling the incredibly vast amount of information required to "disassemble" and :reassemble" a human being or other life form. To transport something, the system must scan, process, and transmit this pattern information. This is analogous to a television, which serves as a conduit to the vast amount of visual information in a normal television transmission.
(Note: This was written when all TV was still analog and DVDs were not yet out -- and remember that we could transmit TV signals before we could actually tape and keep them.)
Continuing to quote from the same passage:
Storing that information, however, is another matter. In our analogy, it would be like comparing a television (which is incapable of storing an image) to a videocassette recorder, which can store a relatively low-resolution recording of a television program. In order to store the patterns for a human being, one would have to record not only all the atomic and molecular configurations, but all the quantum and energy states of all the electron shells, and the brownian motions of every sub-atomic partical of every atom. While we cannot store all of this incredibly complex information, we can use it as it is being handled in real time.
So the information and matter taken from the original and needed to reconstruct the duplicate are taken from the original as it is dismantled, then place in the "stream." (I consider that a loose term, since all of it, matter and energy, goes through the pattern buffers and through an actual stream confined by the annular confinement beam, or ABM.) We can skip all the steps and say the stream goes from the original, through a bunch of stuff, to the new version, wherever that is. And once there, it is assembled, particle by particle, in the new location.
Now, we know what even solid matter is mostly empty space. So it wouldn't be hard, each time a particle is put in place, to use some kind of force to repel any in the way. While it's never stated this is done, this process takes an actual particle and places it in the new location, then places another molecule, and another. Since the molecules are not going through some kind of energy/matter conversion or anything else, but they are just molecules, if something were done with the matter in the area, we'd see some kind of explosion form the energy. (Either particles would be split, merged, or otherwise messed with at a sub-molecular or sub-atomic level.)
So the air molecules would essentially have to be moved aside for construction of the solid (or liquid) form out of molecules flowing out of the ACB.
This would also explain why someone could partially materialize in a bulkhead or something. Even in a rock, there's still space between molecules. I don't remember if we've seen a person or object that materialized in another object, but I seem to recall, it looked like the two parts were just melded together, with one coming out of the other.
If anything were done, such as "destroying" the particles that were there, we'd see indications of either explosions or significant radiation, which would make using the transporter too many times dangerous.