Learning some very basic theory also helps in transcription. When you can listen to a song and understand it's in a major key, that immediately narrows note choices down, and harmony is easier to figure out because harmony is generally written diatonically. When you understand what intervals are and are able to identify them, it's easier to figure out a melody. You can go note by note pretty efficiently when you know your intervals.
Same with rhythms; if you know about time signatures and understand how meter can be broken up and organized, it becomes easier to figure out syncopated lines.
Unless you're absolutely tone-deaf, transcription by ear is a skill you can easily hone with practice and honestly, it's less about super-mega-talent and more about having the tools to be more efficient with your "guesses."
I do everything by ear.