This is discussed at some length in the film's official novelisation which seems to have been based on an earlier draft script for the film and contains various scenes not seen in the film, notably dialogue scenes involving the Drej.
In short, the research being conducted by Sam Tucker (Cale's father) came to the attention of the Drej Queen. Her spy detected that humanity was about to gain access to the same technology that they use to power their massive hive-ship. Her reaction was swift and pitiless, only they, of all the races in the galaxy, must have access to this technology. Humanity must die
Scout drone Zil-three, called informally "Heshach," prowled through
the underground facility on the planet called Earth.
The-Human-Sam-Tucker shut off the latch switches and stepped back
around the shield he'd gone behind. There on the opposite side of the
table sat a box which looked exactly like the one he'd pointed the
"Eureka!" cried Sam. "I've got it!". He leapt up and danced around the room.
The Queen at the time had recognized the obvious danger.
Biobods had discovered Artifact technology. Her conclusion had been fast and decisive.
So the Earth had been destroyed just as soon as the Alahenena could
By the time the Drej arrived on the scene, Tucker Sr. had already implemented the "artifact" tech in a ship, the Titan. When the Drej were unable to destroy it, the decision was taken to acquire it and study it to see whether it could be used to make more Drej ships, hence their decision to track Cale rather than merely killing him.
Interestingly, the (licensed) Dark Horse prequel comic 'Titan A.E. Part 2' offers a slightly different interpretation; The Drej have detected an unusual energy signature emanating from Earth. They find this energy irresistible as it will allow them to breed a large number of new Drej. Unbeknownst to them, the energy isn't found in the planet but is in fact housed on an experimental starship, the Titan.