Global Uni rankings have a big bias toward research. What the poster is saying is that Germans do more of their research at these institutes than at their Universities so German Universities rate poorly on global lists.
As you can see, in Germany and France, research institutes take the place of what in the US and the UK would be universities like Harvard, MIT, Oxford, and Cambridge. Fraunhofer doesn't even show up, because while they do a lot of amazing stuff, they aren't under publish-or-perish constraints (they instead have contracts to fulfill) and so they publish comparatively little.
This has a number of reasons, some of which are pragmatic. For example, if a French or German university wants to hire a professor, that professor usually has to be able to speak French or German, respectively, at least at a near-native level to be an effective teacher (there are exceptions, but it's still a frequent requirement). Research institutes aren't constrained in this fashion, even though they closely interoperate with universities.