It's not happening in the mosques that I frequent, but no doubt that there are mosques where extremists congregate. While I personally haven't witnessed any of this, you can see from the news that there is a small, but very vocal, group of hard core conservatives in Indonesia. But, as I said, I've never witnessed this on a personal basis. I do have several short stories, however, about the opposite.
Just a quick story that I may have repeated once somewhere on this forum...
A few years ago, a stranger wandered into the village asking somewhat vague questions about foreigners. Some neighbors reported this to me as they noted that they didn't want troublemakers in "our" village; I reported it to our security who reported it to the police. The poor guy was promptly picked up and interrogated. It turned out he was a traveling salesman.
In a similar vein, during all the tension a number of years ago about "sweeping", people from my mosque in Bali stopped by the house one day to tell me that anyone coming into our neighborhood suggesting such a thing would be quickly taught a lesson about good relations between foreigners and Indonesians.
The point is that people do take care of people here, and the good guys do have voices, albeit not as loud as the bad guys.