First of all, most of the time Sabertooth and Toad stayed at that place where Magneto lives. This house appears to be protected from Professor X's brainwaves. This is why we can see Magneto wandering in that house without his helmet. Here is the picture of him from the movie.
Perhaps this is the reason Professor X can't track them.
Another possibility is that he never needed to.
He first used Cerebro for finding Rogue. That's when he also went to railway station to save her. After that, Senator Kelly went to Xavier mansion. That's when Charles looked into his mind and found the base of Magneto. However, finding Magneto's place wasn't as important as destroying the machine that turns humans into mutants.
When Senator Kelly dies, Professor says,
I am going to find her.
Here, he is going to find Rogue and that's how he can reach Magneto. However, he fell into coma because of Mystique's sabotage before he could locate Rogue.