The purpose of amusement licenses is to get you in front of the town and public for approval, not for revenue. They add in the fee to cover the "administrative costs" of doing so. Some make this fee absurdly high in order to discourage amusement devices (I've seen as high as 200/machine/year). Many towns (at least here in MA) will require that you put a public notice in the newspaper, as well as have a public hearing before you can get a license.
Lets face it - pinballs are noisy, and decades ago they attracted teenagers and loitering. I can understand the noise aspect - if I'm operating an art studio and a pinball arcade moves in next door to me, that's not really fair is it? Commercial real estate isn't normally built with soundproofing in mind.
In MA it doesn't matter if you're a retail establishment or an arcade. If you have an amusement machine that is available for the public to play, even if it's for free, then it requires a license.