Like you, I didn't pay the story much mind of the story until I had an opportunity to read Gates's actual remarks, available here.
Gates begins his commencement address by joking about his (lack of) college experience, but the mood quickly turned somber when he expressed his one big regret about his time at college: "I left Harvard with no real awareness of the awful inequities in the world," adding that it took him "decades to find out" about the unbelievable levels of poverty and disease that only grow worse in developing countries.
Gates spends the next twenty minutes expressing his disbelief at the levels of inequity he has experienced in the world and of his efforts to better understand the issue and raise awareness through advocacy. Here is an excerpt:
If you believe that every life has equal value, it’s revolting to learn that some lives are seen as worth saving and others are not. We said to ourselves: “This can’t be true. But if it is true, it deserves to be the priority of our giving.”
So we began our work in the same way anyone here would begin it. We asked: “How could the world let these children die?”
The answer is simple, and harsh. The market did not reward saving the lives of these children, and governments did not subsidize it. So the children died because their mothers and their fathers had no power in the market and no voice in the system.
It's an impressive speech made all the more powerful by the fact that the Bill and Melinda Gates Foundation has an endowment of more than 33 billion dollars. Of which they recently gave more than 10 million to Purdue University to improve food storage techniques in ten African countries.
Video of the afternoon commencement exercises (with Gates's speech at the end) is available for download here.