Most of these answers are somewhat right but pretty incomplete. All design choices are a tradeoff, and that’s even more true for aircraft. I’ll be mostly focusing on airliners with turbofans for this comment. Generally speaking, there are two main concerns: cruise efficiency and controllability in low speed flight. Generally cruise efficiency is going to be somewhat more important in airliners. For simplicity’s sake, I’ll be calling the air ejected from both the core and the fan “exhaust”.
If you’re designing a plane to fly efficiently at 75% to 85% of the speed of sound while still being able to land on short runways, the handling characteristics are going to be a little pathological in some flight regimes, so auto trim systems and pilot training mean that the effect of thrust angle on controllability isn’t usually the overriding concern unless it’s extremely bad. When it does come up, it’s generally because newer engines were fitted to a new variant of an old design. This is what happened with the 737-MAX. The engines being more powerful were a factor, but the main issue was that there’s little room to fit such a large engine under the wing of the 737 because of how the landing gears are designed. This required them to mount the engines forward if the wing, which at larger angles of attack could cause the intake cowling to catch the air and force the plane to pitch up. (While the MCAS system was to counter this pitch up tendency, Boeing had found that the effect was something pilot training alone could adequately address, it was just that pilots would need time in the simulator to adapt to it.)
So in cruise flight, the wing has to be tipped slightly up to make lift. This doesn’t necessarily mean that the fuselage is also tipped up, as the wings can be constructed with enough angle of incidence to keep the fuselage level, but as a general rule the nose of the plane will be tilted up relative to the oncoming air. You waste some amount of thrust if the engine exhaust isn’t aligned with your direction of flight. It’s also worth mentioning that the local direction of the airflow around the engine is disturbed by the airframe. This has some effect on the ideal direction of the exhaust flow, but is a particularly big deal with the intake, as ahead of the wing, the direction of the air slopes up. [This can be remediated by angling the engine intake direction downward.](https://c8.alamy.com/comp/EPT8R2/side-view-of-a-boeing-787-jet-engine-manchester-airport-EPT8R2.jpg)
The wrinkle to that last paragraph is that the engines aren’t perfectly in line with the center of mass of the aircraft. This means that their thrust (when mounted under a low-wing plane), causes a pitch up moment. Some of this pitching moment is helpful. A stable plane is somewhat nose-heavy, and the elevators/horizontal stabilizers have to push against the lift generated by the wing to counter this, creating drag on both themselves and the wing. Airliners generally trim the whole horizontal stabilizer up and down to account for this, so it’s not as bad as the more crude trimming systems on GA aircraft, but every airframe has a happy zone for drag based on how it’s trimmed. This means that the tilt of the engine isn’t just a function of what the reasoning in the previous paragraph would tell you.
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