Don't remember much, but the action definitely took place in a desert where a group of survivors(?) were living under a cupola, which protected them from monsters living under the sand. Also, I think one guy got there by time machine but I'm not sure. Anyone know the title?
Sounds like you might be thinking of Time Kid (2003).
An adaptation of H.G Well's Time Machine for Nickleodon. Tom's scientist father, overwhelmed with grief over the loss of his wife, invents a time machine. He attempts to go in to the future to find a cure that he can take back in time to his wife, so that she might live. He never comes back, only his time machine. So Tom goes into the future to rescue his dad.
From The Time Machine Wiki:
In 19th Century New Jersey, a young boy named Tom Spender discovers his missing father's Time Machine with a note in the seat, saying that the father was stuck in the future and unable to return home. Tom boards the machine and explores the future, first visiting the year 2002 where he meets one of his descendants, and later the year 11,902.
There, he meets a strange race of people- the Luman, who are a very simple, almost childlike folk who live in a domed community. They also have telekinetic powers. When Tom wonders where the food comes from, he discovers that it is provided by a second race, the Sub-Men. When the Luman come to get their food, the Sub-Men take a Luman in exchange.
It seems that the Sub-Men are using electrical energy from the Luman's telekinetic powers to run their machines. Tom soon befriends a Sub-Man, Zorog, and convinces him that there are better ways for the two races to exist. The two soon rescue Lira, who has been captured, as well as Spender's father, Henry Spender.
Tom Spender uses his father's time machine to travel to a desert-like region in the future, where he encounters the Luman, a primitive race of humanoid creatures living under a dome. In this time period, there's also another race of humanoids called the Sub-Men, who live underground. You can view Tom's first encounter with the Luman around the 21:31 mark in the video below.