It's designed to address the underlying sense of entitlement students at the World's best universities can have. As these places can be so hard to get into, successful applicants can adopt a defensive "I'm here because I'm the cleverest and deserve it" mentality. For somewhere like Stanford, having a lot of (daddy's) money is, for most students, also a pre-requisite to attending. The Author is exactly right, being born into a family with money does not mean you deserve to be there, even if you did work really hard during grade school and college. The Freshman's are enormously lucky to have been given the chance to study at Stanford and it is up to them to earn their place, retrospectively. Society will be the judge based on their future work.
The message is not so much "don't get comfortable because 50% will be gone by the end of the year" but rather more of "Welcome to Stanford. Understand that you are here though very little of your own merit. You have the opportunity to change that if you work hard and focus on the bigger picture of society and not just furthering your own wealth".