Besides mining for resources, Minister Tua suggests in Star Wars Rebels: The Siege of Lothal that there is a secretive reason for the Empire being on Lothal.
"No...There is another reason, known only to a few, and ordered by the Emperor, himself."
What is the "true reason" the Empire are on Lothal?
Unknown. However, there is a very good candidate.
As we know from Ultimate Star Wars, the Death Star used a Kyber crystal in its superlaser. The protagonists of Rebels have seen other signs of Death Star construction.
The Rebels on Lothal sought to prevent a Kyber crystal shipment (probably from Lothal) from reaching the Empire.
From "Breaking Ranks" (Star Wars: Rebels 1x04):
HERA: What's the alternative? Do you want to stop that Kyber shipment or not? You know what the Empire could do with that crystal.
KANAN: Nothing good.
and further
HERA: And we'll only get one shot at this.
KANAN: The Kyber crystal resonates with the Force.
This suggests that Kyber crystals are mined on Lothal, which indicates that they may be supplying them as material for the Death Star.
The repeated references to Lothal's significance to the Empire as a site for mining, the fact that there's a significant hidden Jedi temple on the planet and the fact that under said Jedi Temple is a large cavern where you can collect Khyber crystals would all strongly suggest that the Empire is mining crystals for use in some sort of gigantic super-weapon that uses Khyber crystals as a key component.
