They have to make sure there's no air
where they beam people into - having air bubbles inside you when you materialize would be quite deadly!
So, there must exist some way for the transporter beam to push aside whatever matter there is at the destination. If this mechanism can push away air, any flying insects will automatically be removed as well.
If the matter is too much of an obstacle, the transportee will apparently be "rearranged" so that he nicely fits the available space. People standing straight on a transporter platform will materialize with one leg raised if there's a rock under that leg (say, ST2 and Chekov and Terrell's beam-down). Conversely, people lying on uneven ground will materialize lying flat on the level floor of the transporter after beaming up. So, if there's a really
big insect at the beam-down spot, Kirk will materialize with his arm around
its shoulders, not inside