What are the difficulties and dangers faced by low flying aircraft?
A lot depends on how low you are and what aircraft you're flying, but any low-level flight has some risks and difficulties. Here are some, I'm sure there are others:


If the aircraft loses power you have much less time and distance available to execute a forced landing, and your choice of landing sites will be more limited
You can't see as far ahead so it's more difficult to look out for obstacles and pilotage may also be more difficult in some circumstances
You may accidentally break the law on minimum safe flying height because the terrain changes too quickly, you don't see an obstacle or town until it's too late etc.
There's a greater risk of collision with terrain or obstacles like radio towers, especially if your aircraft is a fast one and you have less time to react
The likelihood of both thermal and mechanical turbulence is higher when flying low, increasing risks of loss of control and collision with terrain and obstacles
If you're scud-running in VMC there's a high risk of entering IMC accidentally, which is extremely dangerous (incidentally, despite the title of that question, even instrument-rated pilots have a poor safety record when they enter IMC unintentionally)
Radio reception may be poor
ATC radar may not be able to see you
Your engine may not operate very efficiently


That's not to say that low-level flying is always a bad idea, but it I think it does require more preparation, alertness and even local knowledge from the pilot.