Water, and unclean handling, are the sources of the contamination. If your source is trustworthy, don't worry. Many of the tomatoes coming into our stores now are from local, small greenhouses, soon some will be from the local organic growers.
The mass-produced field tomatoes used by many fast food chains and sold cheaply (relatively)in the supermarket may be exposed to contamination at several points during packing and distribution, as well as in the field from water sources.

Washing fruit is never 100% proof against Salmonella, microscopic cracks and skin irregularities that can't be seen with the naked eye can harbor bacteria.

People often point, without reason, to imports from Mexico and elsewhere when they look for sources of comtamination. There is no difference in the growing and handling of mass market tomatoes or other produce, whether in Florida, California, Arizona, Texas, or Mexico.

Thorough cooking destroys the bacteria- and taste, vitamins, etc. as well, unfortunately.
(Eggs are a more frequent cause of the illness. Scalding the eggs in boiling water before use is a good method, since the bacteria are usually on the shell.)