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Why do you say, "A bus doesn't travel on water" but you then say, "Garbage collection isn't a profession." What are the rules for when to use "do" (doesn't) and when to use "is" (isn't)?

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I'll answer for the verbs on their own. For verb phrases, that can become pretty complicated and seems to be beyond what you are asking.

The verb is usually acts to declare existence or (perhaps partial) equivalence:

  • They said it wasn't there, but it is!
  • He is just like his father.

The verb do usually specifies an action.

  • He did it!
  • I do pottery; my girlfriend does calligraphy.

Thus:

  • A bus doesn't travel on water. [action]
  • Garbage collection isn't a profession. [equivalence]
  • The bus is traveling on water! [sigh, why I'm avoiding verb phrases 🤓 One could argue that "traveling on water" is a state of being, but I don't want to go there.]
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In Early Modern English, all verbs formed negatives by simply postposing "not":

A coach goes not on water.

Waste collection is not a profession.

In modern English, only auxiliaries (have, be, can, may, will, etc) form it in this way:

I will not (won't) go.

You can not (cannot/can't) go.

He has not (hasn't) gone.

If there is no auxiliary, then except for 'be' and sometimes 'have', you need to add the otherwise optional auxiliary 'do'.

So

A bus travels on water = A bus does travel on water.

In the positive, the "do/does" is optional, and we only use it for contrast or emphasis; but in the negative

A bus does not travel on water.

it is required.

The exception is "be":

Garbage collection is a profession.

Garbed collection is not (isn't) a profession.

In most varieties of English "doesn't be" is not grammatical.

The other partial exception is "have":

When it is an auxiliary itself, it cannot take "do":

I have seen him.

I haven't seen him (not "I don't have seen him").

When it is a full verb, both are possible:

I have a car.

In the negative:

I haven't a car.

or

I don't have a car.

Many people would regard the first form as old-fashioned, especially American speakers. It's more common in British English, but even here, it is usually augmented by "got": "I haven't got a car".

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