Although present continuous seems to be used more often in the course, there are times when present simple is fine. In this sentence, the meanings are basically the same, and both "Why do you not eat the soup?" and "Why aren't you eating the soup?" are accepted.
We have simply one present tense as many other Indo-european languages do. But we also have the verbal aspect which is very powerful.
Old Czech (as other Slavic languages then) used to have perfective and imperfective past tenses, but they were abandoned 500 years ago because the aspect is enough and the tenses were not needed.