The only true way to obtain donuts in-game is through purchasing them, or through several in-game methods. For example, when you level up you get a donut, sometimes two. If you're logged in with Origin, sometimes you can get random messages that pop up and give you donuts. You can also get them through setting Homer and Lisa to "Clean Up Springfield" - a six second task, but this only happens sporadically. The aforementioned Jebediah Statue trick with tapping Homer ten times and achieving the statue and ten donuts works as well. One end-game-style method is when you have achieved the highest level possible, when you acquire enough XP to gain another level, instead of levelling you up you get a screen that comes up with a "Bonus Level Up", which gives you the chance to win one, two, or three donuts depending on which icon you press on. If you get a low amount, you can pay to have another go, but it's not really worth it. The Daily Play Combo and the Mystery Box, plus the premium Homer Buddha, are three other ways to get donuts - all are based on pure luck.
So you see, there are many ways to acquire donuts - and soon you may have those couple thousand.
(If I've missed anything (excluding ways to acquire donuts during events such as Valentine's Day and Xmas), please add them in the comments below).