Your passport is enough to fly, you don't need to have CPF.
From Documents Required for Travel:
Foreign nationals boarding domestic flights in Brazil will need to show one of the following documents:
- A valid passport.
- If you are a foreign national residing in Brazil you must show an RNE (National Registry of Foreigners) or a Protocolo de Renovação (RNE Renewal Procedure) issued by the Brazilian Federal Police.
- A diplomatic or consular ID.
- An original photo ID or valid passport if you are a citizen of a Mercosul member or associated country.
CPF should be needed only when buying the ticket (for tax purposes, as mentioned by Aganju). During check-in, on every website I used there was a checkbox "I'm a foreigner", "I don't have CPF" or something similar, or CPF field should be optional when you enter any nationality that is not Brazilian...
This really seems like a bug on their website. You can try to download their app or simply do the check in on the airport. I'm a foreigner living in Brazil and it happened to me three times already, I couldn't check in on the website, I went to the airport and did it without any issues.
Or, if you prefer, you can generate random CPF using this CPF generator - it returns a fake but valid number (11 zeros didn't pass because the website probably validates the number checksum).