When we quote thrust numbers, we generally quote the max rated takeoff "Sea Level Static" thrust. Boeing has something called "BET" or Boeing Equivalent Thrust - that has certain installation assumptions added in. Generally the numbers the engine company quotes are 'ideal' - and don't include losses from the nozzle and inlet. The nozzle and inlets on subsonic airplanes are usually extremely efficient - better than 99% - but that can still be ~1,000 lbs. on a GE90-115B
The other part that many people don't understand is that turbofans start producing less net thrust as soon as they start moving - the thrust decreases or 'lapses' with forward speed (the gross thrust does go up, but not as fast as in the inlet 'ram' drag). The effect is not small - by 80 knots total net thrust can be down by 10%. The thrust lapse with speed is typically higher with higher bypass ratios - pure turbojets suffer little thrust lapse with speed (which is why aircraft that are designed to be supersonic tend to have either pure turbojets or very low bypass turbofans).
The other aspect is thrust decreases with altitude - pretty much as a direct function of the drop in ambient pressure.
As a result, something like a GE90-115B is producing a small fraction of that thrust at a 39k cruise condition.