Not in a city they aren't. They are an excellent commuting tool that offers much of the flexibility of a car for a fraction of the cost and much better commute time.
OK, I'll need to see a source on increased pollution. I really doubt that a motorcycle is putting out more pollution than an average American-size vehicle. For example, my sport bike gets 59MPG, and I've owned multiple bikes that got >100mpg. Even without a catalytic converter, how is that more pollution than a single commuter driving in a truck or SUV getting 20MPG and likely shedding more road and tire particulate due to the increased weight.
Edit: although the noise thing is valid, I'm perpetually annoyed with the "loud pipes save lives" crowd, that's obnoxious.
Does that include motorcycles that have illegal aftermarket exhaust systems with all emission controls removed in an effort to make them as loud as possible? This accounts for about 80% of them, so it's irrelevant how they function by design.
They might have to be that way to buy them new from the factory.
But the moment it belongs to you and even before you leave the lot, you can have illegal aftermarket exhaust systems installed that not one governing body in the United States, nor most of the rest of the world, will come close to enforcing any noise or emissions laws against.