The reason would be that Elros was a Man even though he was of Elvish descent. Since Elrond chose to be of the First-born his children in like manner were given the choice to choose their fates. Keep in mind why this choice is granted to them:
"In them alone the line of the heroic chieftains of the Edain in the First Age was preserved; and after the fall of Gil-galad the lineage of the High-elven Kings was also in Middle-earth only represented by their descendants." [Appendix A: Return of the King]
In Númenor this lack of choice was begrudged by the descendants of Elros because they began to not want their fate, the Doom of Men.
However, it is said that a Númenorean of Dol Amroth, Imrazôr, wedded an Elf, but I do not think their child was given any such choice, and if he were, he chose to be human. So I'd think the Valar only gave this choice to Elros and Elrond, their parents, and Elrond's descendants.
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"For believe me: the secret for harvesting from existence the greatest fruitfulness and the greatest enjoyment is - to live dangerously!" - G.S.; F. Nietzsche
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