The Doctor is a rogue Timelord and other Timelords have made his life miserable for several seasons in spite of him being "good". On the other hand with the evil and megalomaniac Master they choose not to interfere. Why is that?
The Time Lords left the Doctor alone for years, and it's implied that, somehow, they didn't even know where he was (although that doesn't make much sense), until he involved them directly in the situation of The War Games. At that point, even if they had simply been looking the other way where the Doctor was concerned, they couldn't any more, and had to take cognizance of the fact that he had stolen a dangerous piece of equipment and been using it in an unregulated manner for quite some time.
There are several hints, both in The War Games and later in the series (The Invasion of Time), that the penalty for that theft should have been death, on the theory that any being capable of such a theft is too dangerous to leave alive. The Doctor never really expected to face such a penalty -- even in The War Games he's mainly afraid of simply being made to return to (as yet unnamed) Gallifrey and live out a "normal", boring Time Lord life. That his penalty was, instead, exile with the possibility of parole was actually far better than anything he could have hoped for.
After that, there was a tacit understanding between the Doctor and the Time Lords that they could use him when they felt a need to interfere in something but didn't want to be seen to do so. This can hardly be said to be making the Doctor's life "miserable", honestly, so much as his being made to actually be responsible to someone other than himself for five minutes.
Meanwhile, the Time Lords have not exactly ignored the Master. They haven't even always held themselves aloof from the Master's shenanigans. In his very first appearance, Terror of the Autons, they at least warned the Doctor he was coming, although they did not deign to take a hand themselves. Similarly, in Colony in Space, the Time Lords actively "release" the Doctor from his exile momentarily to deal with a plot the Master is undertaking that had seriously broad implications.
While that's the last time that the Time Lord's hand in the matter is made clear, there are two Sixth Doctor stories (Attack of the Cybermen and The Two Doctors) which suggest that the Time Lords have been quietly nudging the Doctor into situations they need handled ever since, which suggests that some of the Doctor's encounters with the Master may not be coincidental.
Long story short: the Time Lords take their non-interference stance very seriously, even when it comes to their own rogues. They take cognizance of such matters mainly when their own interests are involved or threatened, and otherwise stay out of it. This is really true of both the Doctor and the Master (and also Drax, The Rani, the Monk, and, until the Doctor forced their hands, The War Lord). The only real difference is that the Doctor wound up directly involved in something he needed the Time Lords' help for, and that made them have to start paying attention to him.