If it was me, I'd reply with a certified letter explaining your situation as a developer, how much revenue the app has made to date in downloads and ads. Then nicely explain that you would never knowling violate anyone IP rights, and having reviewed their patent do not believe you are practicing any of the steps laid out in their patents. You are, simply using information published via publicly available Nextbus API.
Then wait.
Lawsuits cost money - no contingency in Canada, so by demonstrating poverty, it's really not worth suing you... period. If they come back with a real legal filing, you can always just shut down the app, or find a lawyer to help you fight.
However, I'm not a lawyer, just saying what I'd do... you situation may be different - and getting a lawyer never hurts (except the pocketbook).
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My situation; inventor, lived in Canada for years... now in the US. Your app doesn't appear to be infringing (it's not doing all the stuff laid out in the claims, but the API provider most likely would be, which is why they settled)... however...
1. Canada doesn't do contingency for legal stuff, you will need to find a lawyer and need to pay up front. Get a lawyer (if you want a suggestion ping me at sean@maclawran.ca)
2. I'd talk to NextBus about their API and license. I'd also look carefully at whatever agreement you have with NextBus about the use of their API (free/paid). If anything, Nextbus may be infringing on their license by publishing the data. Alternatively, there may be language in the contract indemnifying you. Look at all the contracts, period.
3. Look carefully at the document you were sent. It will have valuable clues; have they actually filed anything, etc.
If you're using their public XML feed/API, here's the agreement: http://www.nextbus.com/xmlFeedDocs/NextBusXMLFeed.pdf.
Good luck.