For example, if I started a service like AirBnB and all my initial customers were in Boston, then I could wind up being locked into only operating in Boston (under my chosen name) if another company later registered the name.
For consumer web-only startups, you might be able to get by with just a domain name, but it's a risk that in my mind isn't worth the cost savings. Yes, a domain name registration and accompanying web site can be used as proof of use in commerce, but it's not a guarantee and it doesn't help very much with geographical restriction.
You'd be surprised how often people wind up with conflicting names. For a few hundred dollars you can ensure that a huge headache down the road doesn't happen. It's cheaper to get the registration at the start than to litigate later or have to change your name.