The evidence comes from what Lauto tells Link
In order to return the power to repel evil to
your sword, you must find another to take
my stead in this temple and ask the gods
for their assistance.
You must find the one who carries on
my bloodline... The one who holds this
sacred instrument...
Nothing can stop the flow of time or the
passing of generations...but the fate carried
within my bloodline endures the ravages of
all the years. It survives.
That and the use of Nayru's symbol, the same as the Zora has lead people to believe that they are related. However the Nintendo Gallery gives us some different information regarding their origin.
Koboli
Birthplace: Windfall Island
Occupation: Mail sorter
Koboli is the third generation in a family
of postmen, but rumor has it that an
ancestor of his in an age gone by was also
a postman...
Which would connect
To me this is slightly clearer evidence as an ancestor is listed. Plus the one thing that always made me question the Rito Zora origins was the fact that they look a little too human. At least they carry more human features than the typical Zora. They have hair, pupil eyes (although this has changed since TP) skin like a humans while Zoras have scales, and ears.
In fact Red eyes, dark skin, and white hair seems to be a common trait among all Rito, other than Medlii who has red hair.
And we learn from gaining the grappling hook that they were once a non flying tribe that still must gain their wings magically from Valoo. Whick actually led to to look for other evidence of who might have become the Rito by the time of Wind Waker. First I looked to the Gerudo. They have a darker skin and very beak like noses in OoT. But they also commonly have yellow eyes and red hair. And no not have the Hylian pointed ear. So then I looked to someone else using the same characteristics. Who else has darker skin, red eyes, white hair, and was known to live at the base of Death Mountain?
Then all of a sudden owning tools like a grappling hook to get around Death Mountain seems to make more sense.
Of course all of this is speculation piled upon speculation using pics from two separate games as my evidence.