More correct is "For whom or FOR what are you waiting (for)" with the final "for" an emphasis, and not the king's English, but is used just because "waiting for" is so often used together that it sounds right even when doubling up on 'for'. But yes, literally, it could be translated "For whom or for what do you wait?" Both languages are very flexible.
In response to a few comments asking why translations using the simple present -- like "Who or what do you wait for? -- are not accepted, it is because they sound strange.
While the single Czech present tense can translate to several English tenses, when you translate to the simple present in a sentence like this, the resulting sentence sounds like something is missing -- like it should be, for example, "Who or what do you wait for... after class on Wednesday afternoons?"