"Flying" was not an unique trait to Vingilot. After the fall of Numenor the Valar reshaped the world, so that only elven ships following the "straight road" could reach the undying lands. (This happened long after the voyage of Earendil):
The ‘immortals’ who were permitted to leave Middle-earth and seek Aman
— the undying lands of Valinor and Eressëa, an island assigned to the
Eldar — set sail in ships specially made and hallowed for this
voyage, and steered due West towards the ancient site of these lands.
They only set out after sundown; but if any keen-eyed observer from
that shore had watched one of these ships he might have seen that it
never became hull-down but dwindled only by distance until it vanished
in the twilight: it followed the straight road to the true West
and not the bent road of the earth’s surface.
Tolkien's letter no. 325 (emphasis mine)
It is my understanding that the ships do not really fly, free to choose their altitude; rather that there are certain passageways in Tolkien's universe that are intangible and invisible, but can be navigated by a ship, when it has been hallowed. That does not necessarily mean the ship is in any form physically altered, merely that the Valar permit it to use that road. (Although the quote does talk about specially made ships, so perhaps some alteration is required.)
The straight road was one such passageway that many elven ships could use. The "oceans of heaven" were another passageway, and the only ship reported to sail it was the Vingilot, but that does not mean it was altered to become a flying vessel, different from the other elven ships sailing the straight road.