I remember reading somewhere that the tomato was called a "Poison Apple" or "Poison Love Apple", and that there were some misconceptions about green apples.
The poisonous myth actually comes from multiple sources; The use of pewter tableware was a large reason. Pewter is an alloy that typically contains small amounts of lead. This is usually harmless, but the highly acidic tomatoes tended to leech out and absorb the lead from the plates, leading to some horrible cases of lead poisoning.
It's the most sited, that wasn't the only reason. Tomatoes are in the Solanaceae family of flowering plants, which contains a great deal highly poisonous plants. The plant itself (stems, leaves, roots) also contains amounts of the chemicals Tomatine and Solanine which are deadly in large amounts. (Solanine is also found in potatoes) However, the concentrations are usually low, but due to association, tomatoes were assumed to be poisonous as well. (The aforementioned lead poisoning certainly didn't help it's reputation)
The poisonous nature of Nightshades was well known, and highly documented. The Romans used it extensively as a method of assassination and execution. The Atropa Belladonna is one of the most toxic plants in the Eastern Hemisphere, consumption of 2-5 berries is enough to kill a fully grown, healthy adult. Many Nightshades are also hallucinogenic and give "visions" and "sensations of flight" which lead to their association with witchcraft.
In fact, the witchcraft association was so strong, the scientific name for the plant lycopersicum literally means "Wolf peach" due to it's association with werewolves and lycanthropy.
Even when the superstitions began falling out of favour, the negative associations with the plant stuck around for a long time.
The high acid content led tomatoes to absorb lead from the platters it was served on, which meant you could get lead poisoning from them. Not true if you know not to use lead plates.