Fascinating article. I think it overstates the case a little. I hear Indonesian I can understand when I hear two Indonesians talking to each other (when I'm not part of the conversation, I'm just eavesdropping), which wouldn't be the case if things were as bad as the author claims. But yes, there is a lot to relate to in the article.
A lot of kids growing up now in Jakarta speak only Indonesian and may not be able to speak the regional language/dialect of their parents with any fluency (although they may well understand it). Then there is a small subset of Indonesian kids at international schools for whom English is their first language and they cannot speak Indonesian properly (never mind any dialects). This is due to their parents speaking to them in English, despite being Indonesian.