Yes, you are correct. Generally when we use this expression the point is "don't think of me like that." Although usually there is a look involved first, which leads to a person thinking that they know what you feel towards them.

Thank you, Rich. If someone judges me for something I've just done, I say "Don't look at me like that". In this case, is it equal to "Don't think of me like that/that way"?

It’s an aggressive defensive question as the person thinks you’re staring at them or looking disappointed or judging for something they’ve just done