Bad code can certainly be part of it. The average skill level of those coding C/C++/Rust tends to be higher. And modern programs typically use hundreds of libraries, so even if your own code is immaculate, not all of your dependencies will be.

But there's other reasons, too:

• Python, Java etc. execute their compiler/interpreter while the program is running.
• CLIs are magnitudes slower, because these languages require a runtime to be launched before executing the CLI logic.
• GUIs and simulations stutter around, because these languages use garbage collection for memory management.
• And then just death by a thousand paper cuts. For example, when iterating over text, you can't tell it to just give you a view/pointer into the existing memory of the text. Instead, it copies each snippet of text you want to process into new memory.
  And when working with multiple threads in Java, it is considered best practice to always clone memory of basically anything you touch. Like, that's good code and its performance will be mediocre. Also, you better don't think about using multiple threads in Python+JS. For those two, even parallelism was an afterthought.

Well, and then all of the above feeds back into all the libraries not being performant. There's no chance to use the languages for performance-critical stuff, so no one bothers optimizing the libraries.

At least with Java, its the over(ab)use of Reflections and stuff like dependency injection that slows things down to a crawl.