It's not the case. Effective altruists give to dozens of different causes, such as malaria prevention, environmentalism, animal welfare, and (perhaps most controversially) extinction risk. It can't tell you which root values to care about. It just asks you to consider whether the charity is impactful.

Even if an individual person chooses to direct all their donations to a single cause, there's no way to get everyone to donate to a single cause (nor is EA attempting to). Money gets spread around because people have different values.

It absolutely does take some money away from other causes, but only in the sense that all charities do: if you give a lot to one charity, you may have less money to give to others.

The general idea is that on the margin (in the economics sense), more resources should go to the most effective+neglected thing, and.the amount of resources I control is approximately zero in a global sense, so I personally should direct all of my personal giving to the highest impact thing.

And in their logic the highest impact is to donate money, take high paying jobs regardless of morality, and not focusing on any structural or root issues.

Yeah, the logic is basically "sure there are lots of structural or root issues, but I'm not confident I can make a substantial positive impact on those with the resources I have whereas I am confident that spending money to prevent people (mostly kids who would otherwise have survived to adulthood) from dying of malaria is a substantial positive impact at ~$5000 / life saved". I find that argument compelling, though I know many don't. Those many are free to focus on structural or root issues, or to try to make the case that addressing those issues is not just good, but better than reducing the impact of malaria.