Is it obligatory to obey one's parents if they refuse their son's marriage to a girl who has no fault other than her family not being highly educated, even though she is religious and of good character?

The religiously recognized compatibility is in one's faith. If the young man's family refuses his marriage to you, he must obey them. A woman's marriage is not valid without a guardian (wali). You must sever ties with this young man and repent to Allah.