Many modern airliners have safety features built into certain systems that actually work against you in some circumstances. (Unless otherwise noted the systems described are for the Dornier 328 Jet).
The first system is the brakes. When I was undergoing training years ago in light aircraft you would frequently see a brand new tire with a flat spot on it caused by a pilot landing with his feet on the brakes. The same pedal that operates the rudder in the air operates the brakes on the ground (brakes are operated with toe pressure - rudder is operated with heel pressure). In order to prevent this our brakes do not work AT ALL after landing until the airplane has sensed that it is on the ground or the wheels have spun up to 30 knots.
The 2nd system we'll talk about is ground spoilers. These are panels on top of the wing that pop up after landing to reduce the lift of the wing to make the brakes more effective. Needless to say it is a very bad thing for these devices to deploy during flight so certain safeguards were put in place to prevent this. The spoilers on my plane will not deploy unless the throttles are back near idle, the landing gear is down, the aircraft senses weight on wheels and the wheels have spun up to 45 knots.
The final system we'll talk about is thrust reversers. These allow thrust from the jets to be directed forward to help the plane stop. Again, this is something you definitely don't want activating in flight. My plane doesn't have this feature so I'll speak in general terms. The safeguards are usually similar to what I described above. The airplane needs to know it's on the ground either through "weight-on-wheels" logic or wheel spin up logic or both.
None of these are really unsafe but they can bite you if you get sloppy when landing on a wet or icy runway. The problem usually begins by flying the final approach a little too quickly. This causes the airplane to land farther down the runway. The second trap you can fall into is if you try to make a nice smooth landing. By holding the plane off to "grease it on" you eat up still more runway and when the airplane does get on the ground it has touched down so softly that it takes longer for the "weight-on-wheels" sensors to detect that it's actually on the ground and for the wheels to spin up.
I read about an accident where all three of these factors came into play. The airplane landed quite far down an icy runway and, after it landed, neither brakes, spoilers, or reverse was available to help it stop and it ran off the end of the runway.
The safeguards I mentioned are not difficult to work around. Quite simply, when operating from shorter runways you fly the correct approach speed, touch down quickly and firmly, and then apply max braking and reverse.
Just a note: I am not saying this is what happened in the Brazilian crash.