Yes I've wondered why Firaxis gave resources the bonuses they have. It's frustrating that many plantation resources give 4-5 commerce at a time when a cottage would be giving the same yield, and cottages will improve with printing press and free speech, so plantations actually reduce your commerce, they negatively affect your output. That rice gives less food than wheat is just probably some stupid arbitrary decision made on the part of the developers. Also, late game resource yields are painfully low. IMO oil should have a higher yield than gold, it is certainly more valuable, but again, its yield is so low that it actually reduces output.
As for Euro-centricism, it's possible that's what's going on here, but even then the developers failed hard. Wool and cotton were key components to jump starting the industrial revolution, as Europe borrowed and improved upon spinning techniques from elsewhere in the world, and eventually European spinning machines produced decent quality stuff in a fraction of the time. If we wanted to replicate a European advantage we'd have to make wool the best resource in the game, like 10 hammers and 10 commerce.