Codo-san Konnichiwa! :P
Yes, this is a bit tricky. Let me try to explain:
Note the following - U-ending verbs:
*tsuka__u__* _"to use"_ :arrow: drop the 'u' and add 'eru' :arrow: *tsuaka__eru__* _"can use"_
*ik__u__* _"to go"_ :arrow: drop the 'u' and add 'eru' :arrow: *ik__eru__* _"can go"_
*hanas__u__* _"to speak/talk"_ :arrow: drop the 'u' and add 'eru' :arrow: *hanas__eru__* _"can speak/talk"_
To form the polite versions of these three "CAN" verbs (*tsukae__ru__, ike__ru__, hanase__ru__*) you need to replace -RU with -MASU, so you get *tsukae__masu__, ike__masu__, hanase__masu__*. And, to make these questions, we just add the particle -KA :arrow: *tsuakemasu ka? ikemasu ka? hanasemasu ka?* _"Can you use?" "Can you go?" "Can you speak?*_
Now, *taberu* or _"to eat"_ is a -RU ending verb so to form the CAN-verb we need to follow these rules:
*tabe__ru__* _"to eat"_ :arrow: drop the 'ru' and add 'rareru' :arrow: *tabe__rareru__* _"can eat"_
To form the polite version of *taberare__ru__* _"Can eat"_ we need to replace -RU with -MASU - which gives us *taberare__masu__* _"I can eat"_. To make this a _CAN YOU?_ question we add the question particle KA :arrow: *taberaremasu ka?* _"Can you eat?"_
:idea: As you can hopefully see, *tabe masu ka?* does not ask _"CAN you eat?"_ but rather _"DO you eat?"_ and hence is NOT a "Can you?" question.
Hope that helps!