1) Value of life vs. value of species/society
While I think what Bill Gates does is absolutely a noble cause and will improve the lives of millions (if not billions), it is not necessarily the most effective way to fix humanity.
I say this because of #2, leverage. Levers as in force multipliers, as in things that have a meaningful impact on the world. Currently, the largest levers on the planet seem to be corporations and most of the corporations have very selfish, short term goals. This is nothing short of a tragedy and if we can apply a few multi-billion dollar levers appropriately then our world will almost immediately become a much better place.
You can argue that the hyper loop is a first world problem and doesn't help the majority of the impoverished world. Here's a counter point for you: One of the main reasons we don't ship off all the food wasted in the US is because transportation sucks, if we had a hyper efficient means of transportation then all sorts of options open up for moving food and other goods (water?) to areas in need.
The fact is, cheaper and more efficient transportation/communication breaks down barriers and has a stabilizing effect on humanity. Cheaper and more abundant power results in higher quality of life. New medical tools and techniques eliminate suffering. Anything you can do altruistically, you can do far more efficiently (and more sustainably) with a proper technological solution.
Luckily this is not an either/or and approaching the problem from both ends is obviously ideal.