Is there a difference in meaning in the following two sentences. "Why are you learning Spanish"? and "Why do you learn Spanish"?
There can be a distinction in meaning, but there is no guarantee that the speaker is making it.
Why are you learning English?
That question can be asking why you have chosen English over French, say, or Russian. What are your reasons, at present, for choosing to learn English?
The simple present can refer to a general state of affairs, and so the following question could be a kind of rhetorical question:
Why do you learn English? You learn English to be able to communicate with people all around the world.
That question might be paraphrased "Why would anyone want to learn English?" or "What are the practical reasons for one to choose to learn English?" The "general state of affairs" aspect of the simple present pushes you towards one, or at least it admits that meaning of you whereas the continuous/progressive does not.
"Why are you learning Spanish"?
Good. This seems to be the standard, idiomatic way to ask such a question. The present continuous form of the verb, which matches the ongoing process of learning a language.
"Why do you learn Spanish"?
Not as ideal. This gives the impression of a non-native speaker asking the question. The verb "learn" here is only in the simple present, which doesn't add the nuance that language learning is an ongoing activity.