Just to clarify: I think Brian has confused two of my more recent posts. One, where I said that the absence of Targ traits in Jon's appearance doesn't rule out him having Targ blood, and another where I said that violet eyes and silver hair don't necessarily indicate Targ blood anyway - they can represent other strains of Valyrian blood.
You need to understand that GRRM has said that genetics, as such, don't work in ASOIAF. If they did, the classic 'House looks' and other traits that are passed down 'in the blood' would be mixed up by thousands of years of noble intermarriage in Westeros.
Thus, it's a bit misleading to talk about some House looks being 'dominant' or 'recessive', since these are genetic terms.
House looks can be typically dominant over other House looks, as is the case with Baratheon/Lannister marriages, where every recorded child of the union has had Baratheon looks. But that doesn't make Baratheon looks 'dominant' in general. Stannis' daughter has Florent looks, for example, as does Edric Storm. Everything depends on what blood is matched with what.
So, it is perfectly possible that Stark looks can win over Targaryen looks every time, despite Stark looks usually losing out to Tully looks. The latter does not indicate that the Stark blood is generally weak, or recessive. (Indeed, if it was, it's hard to see how the Starks of the present could resemble the Starks of the past.)
Targaryen looks are hard to judge, as hodor notes, because of the intermarriage. Also, there is some indication that, where intermarriage was impossible, the Targs preferred to find brides with Valyrian blood - which, as I noted above, can mean similar looks. House Velaryon is the example given - they are said to have provided three brides for Targaryens because of their Valyrian blood.
The Dornish marriage that produced Baelor Breakspear was a rare (but not unique) exception to this. In that case, the Targ looks lost out to Martell looks. In the case of Rhaegar and Elia's marriage, GRRM has confirmed that Rhaenys looked like a Martell, and Aegon a Targaryen.
Thus, at least one of Rhaegar's kids didn't look like him. It's not unreasonable to assume that another one didn't either.