"mother" as an adjective could mean being the source or origin of something.
Since the motherboard is the main part of the computer, you can find the source and origin of the device in the motherboard.
So from a linguistic perspective you can find the meaning 'mother' in the word 'motherboard' .
Otherwise you can't find bill in 'billboard' as Jiabao mentioned, nor any eggs in an 'eggplant' .
It shows how peculiar the English language is ;)