Yes, they did. At the very least Pausanias in "Description of Greece" VI, 20, 1 mentions sacrifice for Cronus done once a year on the head of a mountain Elathion in Elis. Sorry, I can't find a reference for English translation of this excerpt.
Talking about Rhea, the late cult of Rhea-Cybele is widely known.
UPD. Pausanias "Description of Greece" I, 18, 7 tells about the temple of Cronus and Rhea in Athens.
ἔστι δὲ ἀρχαῖα ἐν τῷ περιβόλῳ Ζεὺς χαλκοῦς καὶ ναὸς Κρόνου καὶ Ῥέας καὶ τέμενος Γῆς τὴν ἐπίκλησιν Ὀλυμπίας. ἐνταῦθα ὅσον ἐς πῆχυν τὸ ἔδαφος διέστηκε, καὶ λέγουσι μετὰ τὴν ἐπομβρίαν τὴν ἐπὶ Δευκαλίωνος συμβᾶσαν ὑπορρυῆναι ταύτῃ τὸ ὕδωρ, ἐσβάλλουσί τε ἐς αὐτὸ ἀνὰ πᾶν ἔτος ἄλφιτα πυρῶν μέλιτι μίξαντες.
Sorry, I'm only able to retranslate this piece into English from Russian translation.
In this area there are ancient works: the brass Zeus, the temple of Cronus and Rhea, and the sacred circle of Gaia known as 'Olympia'. Here, approximately half-yard long, the ground went asunder and, they say, after the deluge in times of Deucalion all the waters went hither. Because of that, every year they drop hither the wheat flour mixed with the honey.
This text so far is not the evidence that the temple of Cronus and Rhea really existed in times of Deucalion. Pausanias only says that it is situated near the cleft (as comments suggest, the latter does not exist anymore) which appeared in those old times.