For some reason it is easier to understand this idea of electromagnetic waves actually altering what they touch when you are talking about invisible ones like x-rays. It is hard to believe that light - lovely friendly white light - also changes almost every object it hits...
The best way I've found of understanding this is to think not so much of something 'being' a colour but of 'doing a colour'. The atoms in a ripe tomato are busy shivering - or dancing or singing; the metaphors can be a joyful as the colours they describe - in such a way that when white light falls on them they absorb most of the blue and yellow light and they reject the red - meaning paradoxically that the red tomato is actually one that contains every wavelength except red.
Victoria Finley, Colour: Travels through the Paintbox (Sceptre, 2002), page 6.