Putting on your headphones at the office and trying to get work done is seen as a signal that you need to concentrate. You find yourself shut out of critical decision points meetings because people needed to make a decision but assumed you were deep in thought and couldn't take an interruption. Balancing these two needs is hard.
Still sounds like a dick move to me, if the office were on fire and you were taking a nap in the breakroom would people leave you to sleep while they got out to save themselves? probably not.
Thats, an extreme example but if you follow it, you can see that the keypoint here is "critical decision", if you're making decisions without somebody that should be involved in the process, because you're so damned polite that you didn't want to bother them, I'd hazard that you're not really polite at all, you're just being passive aggressive, but I'm a bit of a cynic ;)
One solution is to build a team culture that communicates asynchronously by default, like what 37 Signals describes. This has efficiency costs, but it does seem to work.
Another solution is to co-locate everyone, communicate frequently face-to-face, and build cultural norms that reduce the cost to individual productivity. My team is working on this approach, but we are considering the benefits of remote work and asynchronous communication.
But if "critical decision points" are coming in very frequently - you are probably not delegating work or you have a team that doesn't raise issues in daily meetings, or that simply "can't decide" or "doesn't have the freedom to decide independently" or "do not want to take responsibility to decide for some reason".