This is true; it is idiomatic, but Duolingo cares more about the grammar, not idioms. So, for Duolingo, «Senti quel flauto?» is literally "Do you hear that flute?" and «Puoi sentire quel flauto?» is literally "Can you hear that flute?"
Also, I cannot speak for everyone, but when I mean "do" I say "do." For example, when there was a weird noise yesterday, I asked "Do you hear that?" and not "Can you hear that?"
It's very 'American' English to say 'do' and very 'British' English to say 'can' in an instance like this. I am British and we never say 'do' for this type of sentence. If I were translating the text of an Italian book for a British market I wouldn't even consider it putting 'do' instead of 'can'. I feel grumpy I have lost a heart for this :( ;)
My take on 'can' and 'do' as a native English speaker: the two verbs are interchangeable. However - and this is only my own opinion - I would tend to use 'can' if I was questioning if someone else could hear something that I was unable to hear, whereas I would use 'do' if I was seeking confirmation that someone else could hear what I was hearing. Examples: Me, remotely talking over a radio: "Can you hear anything?" Me, speaking directly to another person after hearing a noise: "Do (or did) you hear that?"
The famous Christmas song from The Little Drummer Boy
"Do you hear what I hear"
agrees with me at least!