Is there any risk of illness from eating a raw tomato?

Yes. Tomatoes may be contaminated with the pathogens E. coli or salmonella, depending on how they were farmed, harvested, or processed. Both pathogens may reside in soil where tomatoes are grown. During harvesting, processing, and distribution, human hands can spread the pathogens from contaminated to uncontaminated tomatoes.  Also, tomatoes may harbor the virus Hepatitis A as a result of poor handling during harvesting, processing, and distribution.  Because viral and pathogenic contamination can occur at any point from farm to table, careful storage and  handling is important once they are purchased.
 
Tomatoes are also prone to spoilage (which can make them look, taste, and/or smell bad)  and mold growth. Do not eat tomatoes showing visible signs of spoilage or mold. Spoiled tomatoes may assume a slimy appearance or texture or feel excessively soft.  
 
Source(s):
FDA "Safe Handling of Raw Produce and Fresh-Squeezed Fruit and Vegetable Juices"
University of California "Tomato--Recommendations For Maintaining Postharvest Quality"
Texas A&M University "Safe Handling of Fresh Tomatoes"