In Star Wars, the first guiding light in Anakin Skywalker's life was his mother, Shmi Skywalker. She taught him right from wrong, kindness towards all things and to have hope above all else. While they were slaves, Shmi made sure to remind Anakin that his mind would always be free. Ultimately, she was the one who gave him the courage to join Qui-Gon Jinn and Obi-Wan Kenobi and become a Jedi.
Years would pass, and Anakin's training would take him all across the galaxy with his master, Obi-Wan. However, he would often have dreams of his mother being in danger. Anakin, against his master's wishes, would make his way back to Tatooine to find her. Unfortunately, he was too late. By the time Anakin could get to her, she had been tortured nearly to death. Shmi died in Anakin's arms and was buried next to Owen and Beru's future home. But decades later, her grave marker vanished. The reason for this would serve to twist the knife in Anakin's broken heart.
Shmi's heartbreaking death was the beginning of Anakin's descent into the Dark Side. After she died, the young padawan used his lightsaber to kill the Tuskan Raiders that took her. This included the woman and the children as well. The decision would stay in his mind and be the first of many hard memories he would return to.
Anakin Skywalker's defining feature has been his ability to carry so much pain and sadness while continuing to live on. It's unclear if this is a positive or negative quality, but it allowed him to fight his way out of the Dark Side when his family needed him most. His ability to never give up, even when he wanted to, was probably taught to him by his mother.
For decades, Anakin never returned to his sandy home planet. When he finally did, he did so as Darth Vader. While uncovering the secrets of how his son grew up in the Darth Vader comic series, Vader managed to locate the plot that his mother was buried in. According to the droid that accompanied him, the marker for her grave was moved by Owen and Beru to keep his mother's life from Luke to protect him. The idea was originally introduced in the Legends story, A New Hope: The Life of Luke Skywalker, but has become one of the many ideas brought over to the main canon.
The decision to hide his mother's grave hurts him more than anything else could. In many ways, his mother's grave is the last place anyone could find what was left of Anakin's soul, and even that was hidden from the world. There is no doubt that her grave marker's moving gave Vader feelings of regret for how he wasn't there for the family that is now gone.
Anakin was too young to leave and too old to join the Jedi. In many ways, the universe had a lot going against him. However, thanks to his mother, he was able to beat the odds and become one of the Clone Wars' greatest heroes. But that attachment would also lead to his turn to the Dark Side. Anakin's mother always kept him strong, and when she died, part of him died too. Covering up her gravesite symbolizes hiding one of the few highlights of Anakin's life and only serves to further Darth Vader's tragedy.