"Never. You will wed the king."
Okay, the title is a misdirection, as this isn't about Maggy's Prophecy. It's more on the Martells' misplaced loyalty to the Targaryens. But still! The tension between marrying the prince and marrying the king is relevant.
Prince Rhaegar was the eldest son of the king, and he married Princess Elia Martell.
Again: he was the eldest son of the king. He was next in line for the throne. When he became king, Princess Elia would have been his queen. Her son would have been the next king after that.
Who knows what kind of interactions the Targaryens had with the Martells before the rebellion? And really, who cares? That marriage joined House Martell of Dorne to the royal family. It meant their blood would become royalty. No other House in the realm could have given the Martells what they had with Prince Rhaegar.
AAAAAND then Prince Rhaegar ran off with Lyanna Stark. That was a crappy way to treat Princess Elia and their two children, but nothing could change that she was his wife and she DID have two children with him. Those children were still high up in the line of succession. King Aerys made everything worse and the realm went to war.
The rebels won the war and Prince Rhaegar never became king. Princess Elia and her children were killed in the Sack, and the lord who presented their bodies to the new king was rewarded for their murders. He was rewarded in the form of getting his daughter married to the new king.
Princess Elia would never become queen. Her children would never inherit anything. No, no, Robert Baratheon killed Prince Rhaegar and wedded the daughter of the man who orchestrated the deaths of Princess Elia and the children.
Elia Martell wedded the prince. Cersei Lannister wedded the king.
I can see how Elia's brothers would be enraged at the new regime.
In the period between Rhaegar running off with a younger lady and him dying on the Trident, Prince Doran and Prince Oberyn may have been asking themselves: IS this jackass prince coming back to his marriage to our sister?
But then after he died, they'd never know what he had intended to do regarding their sister and the children.
In the short period of time between Rhaegar's death and the Sack, Elia's brothers may have been telling themselves the Targaryens still had a chance to win the war, and if they did, then their blood was still next in line for the throne.
And then there was the Sack, and their blood ran red through the halls of Maegor's Holdfast.
Before Rhaegar died, Doran and Oberyn may have had some concerns about how he was treating their sister. After Rhaegar died, though, and after Elia and the children were killed in connection with the Targaryens' defeat, then the narrative changed. They'd never know what Rhaegar had intended to do...but from there, it wouldn't have been much of a leap for Elia's brothers to start telling themselves that of course Rhaegar was going to come back and make their sister his queen, but Robert Baratheon made that impossible.
The Martells' blood was supposed to become royalty, but Robert Baratheon killed their royal brother-in-law and joined his House to the Lannisters. Elia never had a chance to be queen, whereas Cersei went straight to queen. She got the position Elia should've had. House Lannister got the position that should have gone to House Martell.
After the losses their family suffered, I can understand how the Martells would look at the new Queen Cersei and hate her. From there, it wouldn't have been much of a leap for Doran and Oberyn to start telling themselves Tywin must have hated Elia the same way, and that's why he had to have her killed.
(I'm sure it didn't help matters that Joffrey looked like he fell straight out of the Lannister family tree, and his sorry ass became the next king.)
Now allow me a digression, on Tywin's relationship to King Robert vs. the Martells' hypothetical relationship to King Rhaegar. Tywin built up an undue level of power as the king's father-in-law...because the crown borrowed so much gold from him. That debt resulted from two factors: 1) Littlefinger was actively sabotaging the crown's finances, and 2) Tywin was the wealthiest man in the Seven Kingdoms. If Rhaegar had become king, it's highly improbable that he would've had such a toxic Master of Coin as Littlefinger. Even if he did, the Martells don't have nearly as much gold to throw around. So, even in the alternate universe where King Aerys II died peacefully and the Martells were the in-laws to the royal family, they would not have had what Tywin had with the Baratheon regime.
POINT IS. I can see how the Martells would be pissed as hell at seeing Cersei Lannister wed the new king. That doesn't mean Prince Oberyn's narrative of Tywin Lannister's motivation holds any more water than a fishnet. I can see how the Martells would come to view Prince Rhaegar as a martyr rather than a reckless philanderer. That doesn't mean the Targaryens were good to them, or that a new marriage alliance with the surviving Targs would benefit the Martells, or that restoring the Targs to the Iron Throne would provide justice.
After the war was finished and Robert became king, I can see how the Martells would start telling a certain tale. That doesn't mean their tale adds up.