In short: Increase residential ratings (and what you can charge for rent).
I believe the only way to make money is to significantly increase (if not max out) the rent. To do this, you need to minimize things that lower the rating (adjacent houses (if 2+)/roads (if 2+)/factories/landfills (if in 3 tile radius), and maybe some other stuff) and potentially use parks to offset the negatives. Parks give at least +2 to all houses in a 3 tile radius; trees are generally useless as they only give +1 to houses they are immediately next to. I believe that "immediately next to" does not include diagonally (for both trees and adjacency penalties). Note that each road costs you $1.20/day (there's pipes underneath it according to the Finance screen), so try not to put one down unless you're going to use it.
Do not use shops if you can help it -- markets give you more money per resident (even if you have to build an extra road tile just for the market). Every upgrade you are offered in shops is actually less profitable per resident, so don't use them if you're struggling for money. Also try to make sure they'll be in heavy use (less than 50% usage and they lose money). It isn't clear, but I think factories actually cost you something like $10/day (this manifests as a decrease in profit in the goods pricing screen) - adding a factory can often make you *lose* total profit, even after you re-optimize the goods pricing screen. Thus, if you get all the way to office buildings, it makes sense to replace a lot of your factories with them. (Higher density residential is also inferior per resident since the rent is per building, not per resident. However, you have to build them eventually because the demand for lower density goes down as you build more of them - there's a screen telling you what residences are in demand.)
When you have everything set up, people will start to trickle in based on the ratings of the house (if it's negative, people leave instead of join) - except sometimes it would take months for people to fully populate an area (with the large housing setting), even with +3 ratings, whereas other times they fully move in before I'm finished building a section.
When you're starting out, feel free to take out loans -- they're not too expensive if you have a good layout -- but do not reach a population of 100 until you have banked up a bit (or at least make a save before you do). When you're preparing to build a new section in your city, be prepared to lose most of your profit until they're all/mostly fully populated/running. (especially if some of them aren't at +3 ratings, at least if you're using the strategy I mention below).
After you're done building a section of your city (with factories/shops/etc), remember to adjust the price of goods. Take it one good at a time and try increasing/decreasing the price until you find the maximum income (you have to jump a day each time to get the new number). Ignoring bugs, the optimal profit is approximately when demand and production meet (note that if your residents have a demand of 10 food, they will be purchasing 10 food, and if you didn't make it in the factories you have to purchase it (done automatically) at some hidden price. Thus, even if you have no factories for a good, you'll want to make sure to adjust the prices to maximize profit.
If you keep all your buildings at +3 star rating for a couple days, something strange happens and you can suddenly charge a lot more for goods. A single residence at less than 3 stars is all it takes for this to bonus to stop (until you get everything back to +3).
There is also a lovely million-dollar-making bug where, if you continue to maintain +3 star ratings on all your buildings, you can eventually get negative amounts of low income people (at least, that's how I encountered it - it took a while to occur, however). The moment this happens, you can start asking any amount for food and - instead of the demand going down, it goes up (since they're "negative" people, the game multiplies the decrease by the negative population, turning it into an increase instead) -- I was even able to set it to $70.00/unit and could have gone arbitrarily high!
Unless you enjoy the clicking aspect of the game, I recommend using a macro like one that can be created via AutoHotKey (free software) - something to let you click 10+ times with a single key press - it took me long enough to build something or experiment *with* the macro as it was! There are unlocks at even 1000 population; I wouldn't be surprised if the clicking part of the game artificially adds dozens of hours to that journey (some buildings cost 30, 40, or even 50 clicks).
One other tip: make sure your layout leaves room for police and fire stations (which both have a range of 12) - you have to protect anything that isn't a road or landfill (at least for fire purposes -- I think only residential needs police). As for landfills, they are like anti-parks in terms of residential rating and *cannot be removed*, so consider saving before placing one. I only barely needed a 2nd one by the time I had over 1000 population - at first it looks like tons of garbage is going into it every day, but this becomes much lower once the city has "caught up" throwing out the garbage.
If you like, I will share the layout I found to be very good.