I know this might sound strange at first but just look at Ruby's hair.
It has the same "black with a little bit red" colour as Raven's hair (You can see it in Volume 2/ Chapter 12. You can't see it on the Team picture with Qrow, Summer and Taiyang, though). Now I don't know this for sure but it doesn't look like Summer has this haircolour and it sure didn't came from Taiyang's side. We can be 100% sure that Summer Rose is Ruby Rose's Mother and we know that Qrow is Raven's Brother. So the only possible explaination for Ruby having the same unique haircolour as Raven would be Qrow being her Father.
Another point is Qrows appearance. Taiyang is sturdy and broad-shouldered (and blond) which fits perfectly with Yang but not with Ruby. Ruby has the same slender figure like Qrow. And their clothing style is very similar. And Qrow taught her his fighting style. And it was stated that he spent very much time with Ruby (and also Yang) and was seen as some kind of fatherly figure.
(Seriously: if I didn't know the show and someone showed me a picture of Ruby and told me to draw a painting of her father, it would be an exact image of Qrow)
And last but not least: Ruby's surname. If Yang and Ruby were both Taiyang's own daughters, why does only Yang have his surname? Why does Ruby have the surname of her Mother?
So this is just a theory, but I think there is a certain possibility. I know: If he really was Ruby's father, why didn't he just tell her? But maybe Qrow was sent to secret missions regularly and just thought he wouldn't be a good father?
What do you guys think?