The differences between what linguists call formal and informal registers is significant, and very important in Brazilian Portuguese. (Disclaimer: I have never been to Brazil, so I'm basing my statement on what I have read in a variety of books about the language, as well as first-hand reports from people who have lived in the country).
Unfortunately, very few learning resources devote enough time to the informal language, at least not for beginning learners. This is probably because it's not always appropriate to use the informal register (for instance, during a job interview or formal business meeting), while it is acceptable to use the formal register, though it might come across as overly stuffy.
Another reason is that it can be more difficult to learn the informal language if you don't have a basic foundation with the formal language. In other words, it's sometimes easier to break or bend the rules of the language if you already know what the rules are.
Here are a couple of examples in English, followed by a couple in Portuguese.
In informal English, we often hear or see "gonna" for "going to," "wanna" for "want to," "kinda" for "kind of," and so on. In each case, trying to reconstruct the original meaning from the informal usage is neither intuitive nor predictable. In the first two cases, the final "a" replaces "to," while in the third one, it replaces "of." I think that it would be harder to teach these informal usages to a non-native speaker than it would be to teach the original, formal versions. Furthermore, in certain situations, the use of "gonna" or "wanna" or "kinda" would not be appropriate, so they have to learn the formal versions anyway.
In Portuguese, you may hear or see forms of the verb "estar" written without the "es-" at the beginning, so that "está" becomes "tá", "estou" becomes "tô", etc. If you started out learning these forms first, and then encountered the full forms, it could be confusing. It's easier to see that "tá" is just a short form of "está" than to try to figure out what the original form of "tá" was if you had never learned "está." Another example is the use of "pra" instead of "para," which occurs both in the spoken and written language. When I first encountered "pra," I thought it was a new preposition that I hadn't learned yet.
So while a beginner should be exposed to the informal language as soon as possible, I can understand why most programs stick with the formal language for the basis of their instruction. I believe that it is relatively easy to supplement one's knowledge of the formal language with exposure to materials that address the informal language, and learners should understand from the beginning that they are learning one form of the language, which might not match what they can expect to hear spoken on an everyday basis.