This is more or less impossible to answer, as there are so many. Apart from acid loving plants like rhododenrons, most plants, particularly vegetables, prefer limey soil or neutral soil.
You'd need to google plant physiology to really understand why some plants prefer one to another, but in general terms it is simply the way the plant extracts nutrients and minerals from the soil. Those that tolerate lime are able to extract minerals and nutrients that for other plants are 'locked up', hence the most common example of bush fruit like raspberries that go yellow on limy soil where they cannot absorb enough magnesium.

its also stems from where they evolved 60 million yrs ago.