In the original SMB and 2JP, blackdrazon is right. The Super Mushroom uses Mario's palette, 1-Up Mushroom is Luigi's and the Poison Mushroom uses the Goombas' so it can vary depending on the stage. The similarity in color between the Super and Poison mushroom (in above ground stages) may intentionally mimic the similarity between several edible varieties and the highly poisonous death cap mushroom which is responsible for the most poisonings.
In the later games, they seeming just made the spot color the main color and made the spots white. This does give the Super Mushroom an unmistakable similarly to the classic fly agaric mushroom (Aminata muscaria), and I suspect that they went backwards from there in recoloring the 1-Up. A. muscaria is poisonous (but not fatally so) and hallucinogenic when raw but is perfectly edible and non-hallucinogenic when properly prepared. They are in fact eaten in Japan particularly around Nagano and traditionally in some Northern European countries. Supposedly the reason they are even eaten at all is because the red type is easily identifiable and impossible to confuse with a totally inedible and poisonous variety.
Purple poison mushrooms are an easy explanation though. Purple is frequently associated with poison in Eastern cultures.