There are some different opinions here, so here's mine:
The words do have a similar meaning, because they both have to do with feeling something in the body.
The sentences do not mean the same thing, as written. But if you write them this way, they have similar meanings:
I clearly empathize with the people who live in those neighborhoods.
The experience of the people who live in those neighborhoods clearly resonates with me.
This story also attracted a lot of loving attention, and resonated with the public.
This story also attracted a lot of loving attention, and the public empathized with the people in it.
[The second sentence about the story makes sense grammatically, but sounds a little odd.]
Empathy refers to feeling what another person is feeling. Something that resonates is anything that makes a person feel, it can be a situation, a thing, or a person.