I am racking my brains but I am sure has to do with a stick and what a Husband did to his naughty wife. The stick he would hit her with was measured by the size of his thumb. If I am wrong, I am sorry, it's just a shame we dont use it more often now.
'Under the thumb' has been used to mean 'in the control of' since the 1700s. I imagine it came about because people would use a thumb to stop papers/banknotes etc from being dislodged/blown off a desk or counter. Since then, it has taken on the meaning of controlling other people, especially if it refers to a husband whose wife controls him!
Fish the Mod, I think you are thinking of the saying "rule of thumb". In days gone by, a husband was allowed to thrash his misbehaving wife with a cane, as long as the cane was no thicker than his own thumb.