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"He never raised his voice. That was the worst thing. The fury of the Time Lord. And then we discovered why.
Why this Doctor, who had fought with gods and demons, why he'd run away from us and hidden.
He was being kind."
-The Family of Blood, Doctor Who 3X09
Kindness was a luxury the Doctor could not really afford. Nine hundred years of traveling through time and space, losing people he cared for and fighting enemies did not leave anyone capable of much kindness and mercy. A thing as simple as meeting a Daleks for the first time could destroy one's morality altogether.
But still being haunted by destroying Gallifrey, he made a special effort to find every bit of humanity - a thing many Time Lords wouldn't have considered a strength - and morality he had in him. Ever since he gave his promise for the first time so long ago, ever since he'd first spoken these words, never cruel or cowardly, never give up, never give in, he'd always managed to find some in him. Mercy his enemies didn't deserve. A second chance no one would ever have given them. But ever since he activated the Moment on Gallifrey, ever since he destroyed his home, it became so hard to do. He almost didn't care about the results of his actions to the other side anymore.
That is, until he met Rose. Rose reminded him of everything he's always loved about the human race, everything he's always found right about them. She was there to stop him whenever he needed to be stopped; to offer alternative ways of action when they were needed; and to give him a purpose when he found none in the whole unending universe around them. She was there to remind him the meaning of goodness and kindness and love.
And now he was alone again. Even though he loved Martha, he could never love her the way she wanted him to, the way he loved Rose. He was trying to keep to his promise, to keep to everything Rose reminded him of, but there was always a line, and with every person he cared for he had lost, the easier it became to cross it. Ever since he lost Rose it became so very easy to cross it.
And the Family did.
When Martha told John Smith about the Doctor, he was terrified. The Doctor wasn't surprised; understanding just how lonely the Doctor was and how merciless he could get at times was more than any human could realize and handle with. John Smith thought the Doctor would never mind watching all these people die for him. John Smith, the human he was for two months, thought the Doctor cared for no one.
But it wasn't that he cared for no one; it's only that he wouldn't show mercy to those who didn't deserve it. He still cared for so many living beings - perhaps too many of them - all those innocent ones, who were guilty of nothing and yet suffered from the consequences of others' actions. All those he always protected and would always protect, but the others... they were the ones he wouldn't mind destroying the way only a Time Lord could. And yet, trying to keep the part of him that was "The Doctor" alive, he still gave them a chance, still gave them the option to escape his wrath, to leave and never return.
But the more enemies who were so set on destroying him they wouldn't mind hurting the innocent, who would stop at nothing to destroy him, he'd encountered, the more people he loved and lost, the easier it was to cross that line.
And the easier it was, the less kindness he showed.