I have done some extensive digging into the subject of their independence, but i´m not quite sure why they remained so, it could have been politics (see; Gerostratus), trade, warmongering or it could have been the Gods their neighbours feared the most.
Gerostratus 350-332 B.C, was king or chief of Aradus whose dominion extended over the northern part of Phoenicia, including the large and wealthy seaports of Marathos and Mariamme. Its title came from the small island of Arados , overagainst Marathus, in which, evedently for security, was the chiefs priciple residence. Probably negotiation had preceded.
The Aradian ships were serving with the Persian fleet, but Gerostratus was ready for a change of sovereignty. What came to general knowledge was that Gerostratus offered to Alexander that allegiance, for himself and his country, which before had been paid to the King of Persia, in token of which he sent a present of a golden crown, which Straton, son of Gerostratus was allowed to place, in public, on Alexanders head, who then proceeded to Marathos.
Archaeologists digging at the site of ancient Amrit (Marathos), have found conflicting evidence to whether the people were Phoenicians, Egyptians, Persians, or Greeks.
The answer is more than likely that the Marathenians lived out their lives in a very cosmopolitan fashion, and were very adaptable and conscious of their geographical location, thus, in the end angering their neighbours, and causing their eventual demise and destruction (see; The inhabitants of Aradus).
The inhabitants of Aradus planned to destroy the city of Marathos in Phoenicia. They communicated secretly with Ammonius, who at the time was viceroy in Syria under Alexander Bala, and offered him three hundred talents to betray Marathos to them. After that, Ammonius sent Isidorus to Marathos, with instructions to pretend he was there on business, when the true reason was to seize Marathos and give it to the Aradians.
The Marathenians feared that the King favoured the Aradians more than themselfs and denied the King´s soldiers entrance into the city. From among their oldest citizens, they selected ten of the most distinguished and sent them as suppliants to the isle of Aradus. These men took along some of the oldest images of their gods that they had in their city, in the hope of thereby appeasing the fury of the Aradians.
The Aradians were extremely displeased and ignored their humble speeches. Disregarding all reverence for the gods, they broke the images and most shamefully trampled them under their feet. When they tried to stone the envoys to death, some of the older men who intervened had trouble getting them to prison safely. The envoys protested and pleaded the privileges of suppliants and of the sacred gods.
Even tho the rights of the envoys were not to be violated, these men were massacred by a company of imputant young fellows. Immediately afterwards, the authors of this villainy came into the assembly. Having taken the signet rings from the Marathenians whom they had killed, they now forged letters to the Marathian people in the envoys names, in which they said that the Aradians would quickly send them some supplies.
They hoped to deceive the Marathenians and have the Aradian forces admitted into their city, in the belief that they had come to help them. For this reason, the Aradians seized all ships belonging to private men, in the fear that someone might possibly reveal their plot to Marathians. In spite of all this, a certain sailor who was a friend to the Marathenians, pitied their sad situation.
He usually sailed in the neighbouring sea. But since his ship had been taken, he boldley swam across the mile wide strait by the night and told the Marathians that the Aradians planned to attack them. When the Aradians realised that their plot had been revealed, they abandoned their plan of sending them letters. Instead, they openly attacked Marathus and captured the city, demolishing it and sharing its territory among themselves.
I know this does not answer completley why the Marathenians remained independent, but does explain why the coins of Marathus disappeared. If i find a documented answer to independency, i will let you know.
The images are of Marathos (Amrit) ruins.