This is a common refrain of many people, but I believe it is rooted in a fundamental misunderstanding of philanthropy and charities in general. They don't really exist to "fix" problems, they are mostly a band-aid over the structural issues that lead to social problems. The long-term solutions to most of these problems involve policy changes rather than "spot fixes"
Like, funding a homeless shelter or the Trevor Project won't fix the problems causing homelessness or LGBTQ teen suicides. But there are enough people with immediate problems who we do want to support them somehow until policy changes happen, if ever.
You're right that the Gates Foundation is one of the few that has achieved some lasting changes, but I would say that is because their MO is quite different from what many NGO's do. This is based on second-hand knowledge from somebody who works there, so I'm not sure if they do this exclusively, but they strongly prefer to partner with the local governments to introduce highly targeted interventions.
This simultaneously makes it extremely slow and frustrating to operate (especially in countries with dysfunctional governments, which is where help is most needed) and ironically reduces the leverage of money (which is a problem when you have a mandate to spend X% of your money annually!) but also means that whenever any change happens it is generally structural and long-lasting.
There are many other organizations that operate with similar long-lasting principles, but it seems to me most focus on immediate, short-term support, which may be a function of the limited funding and skills of the people available to them.