Okay, I think there could possibly be some confusion.
It will depend on how the cells is hidden as to whether Excel defaults to copy visible/not visible. For example, if you physcally hide row 3 and you try to copy and paste the range A2:A4 you will copy Paste that range. If row 3 is hidden due to an autofilter then it will copy A2 and A4 without A3. I could be wrong, but as far as I am aware, there is no way to change that default.
That is where my short VBA comes in handy, but from the sound of the OP's explanation this is not what is occurring here, so I guess there must be some sort of way to change that default.
Edit-
BTW, one quick aside. If the row 3 is physically hidden and you copy paste entire rows 2:4 it will paste all 3 rows as well but will automatically hide row 3. Again this is default on my machine though.