First post here, so bear with me.
1. What I feel you're missing with the payment calculator is they use it as a means of advertising. They bait you in on numbers and get you to try and prequalify through advertised banks. If you really want a more accurate estimate on a payment, use something like mortgagecalculator .org. You can change all of the variables of the loan with it to give you a more accurate estimate.
2. Peraonally I'm more into higher risk rentals that give bigger returns monthly, but don't appreciate in value much long term. Even at "breaking even", your real estate could potentially appreciate quite a bit. Look at values of properties in NYC. A place selling for $2mil right now might have sold for half as much 10-15 years ago. So if you haven't really lost any money on it, and it's almost doubled in value, well, I think that explains itself.
3. Going by your example of a $100,000 property bring in $1,000/month in rent, if you and NOT tge bank actually owned $1,000,000 in property that grossed $10,000/ month in rent. I would say you are doing alright for yourself.