Placement on aircraft that fly above birds. This is the #1 reason we don't hear about airliner bird strikes every day on the news; cruise altitude for airliners is around 30,000 feet, while only two species of bird have ever been recorded flying at that height, one in Central Africa, the other around the Himalayas, neither of these being common travel lanes for airliners. The critical time for most bird strikes is below the cloud ceiling and/or transition altitude, above which the air becomes thinner and birds have to work harder to stay aloft. Airliners spend as much of their flight time as feasible above transition, where the thinner air reduces drag and lowers fuel consumption.
Strong intake fan fins. The first set of turbine fins that you see looking into a nacelle are the ones in the direct line of fire. They're also the largest fins, but in their favor there are higher acceptable tolerances for those fins versus the ones in the compressor stages. So, they're built strong to hopefully survive ingesting your average goose, and the engine can operate at least for a little while with a fan blade broken or even missing.
Garbage disposer effect. At ascent throttle levels, an airliner's engines are rotating between 10,000 and 15,000 RPM. Even travelling at cruising speeds of 500-550 knots, the rotation speed of the turbine will chop most organic matter into mincemeat in a fraction of a second. These smaller pieces cause fewer problems passing through the engine.
High bypass. About 80% of the air volume entering most underwing airliner engine nacelles passes around the turbine chamber instead of through it, increasing thrust while reducing fuel consumption. Fuselage-mounted engines on older aircraft had lower bypass ratios (one of the reasons those designs are being phased out of modern fleets). A bird entering the engine has a similar chance to pass right on through without encountering the combustion chamber.
Reinforced nacelle housing. In the event a bird strike does dislodge something in the engine, the nacelle housing is engineered specifically to contain the shrapnel, minimizing the chance of damage to fuel and control lines in the wings and of course to the fuselage. The pilots will be alerted the engine has failed, and will cut off the fuel supply, engage fire suppression and run on the remaining engine(s).
Overspecification of required engine thrust. One of the major tests an airliner design must pass before being FAA certified is an "engine cutout at decision" test. An aircraft is loaded to MTOW, taxis to the runway, the engines are spun up, the aircraft rolls out, then at the "decision speed" above which the pilot must commit to a takeoff, an engine is idled. The aircraft must still be able to get off the runway and attain a minimum climb rate. That test, for most modern two-engine jets, shows that the plane is perfectly capable of flying on one engine (if such a thing happened at takeoff in real life the jet would circle and land again but it would not have to risk an aborted takeoff above decision speed).
The most famous bird strike incident in recent memory, Sully Sullenberger's emergency water landing in the Hudson River, was caused by hitting not one or two, but an entire flock of birds, and not sparrows or pigeons, but Canada geese, which can weigh up to 20 pounds each. This incident is still a good example of how well engineered these engines are; both engines would have been at full revs as the plane was climbing out of LaGuardia, yet the nacelles still contained the shrapnel, saving the control surfaces and lines for the ditch attempt, resulting in no fatalities and only one hospitalization.