This is the important bit of info:

The message caused outrage among Facebook users, which prompted the group to clarify their warning, saying they did not tell people not to eat tomatoes. "We said don’t cut it in [such a way that it reveals] the cross shape."

http://www.hurriyetdailynews.com/tomatoes-are-christian-egyptian-salafi-...

So Muslims are allowed to continue eating tomatoes. they just need to be careful how they cut them. But who cuts a tomato in that direction anyway?