2003 lincoln navigator. The air ride compressor will not come on. Checked all fusses and relays and they r good. The compressor will run when u straight wire it. Why won't it come on automatically?

I know you stated you checked all fuses and relay and they're ok but The 2003 Lincoln Navigator had two differently (wired) air ride systems. A early production and a late one, and I think I may have a good Idea of what your problem may be and will walk you through how to properly test the system. The early production navigators used a solid state compressor relay and the later production units used a standard style relay. The early ones with the solid state type has been known to have some problems and working for a Ford, Lincoln Dealer for 21 years I have replaced a good number of these solid state relay for a air ride compressor inoperative concern. There seems to be some confusion on the location of the solid state relay. I would advise you to look behind your front bumper on the passengers side of your vehicle (and below your headlight) and see if you have a 4 wire relay that's aluminum and finnd ribs on the front of it and I believe a black base where the wiring connector plugs in. (this will be mounted to the radiator support) if so, you Have got the early production style. I will walk you through how to test this relay and also help you to isolate the cause of your problem. I highly recommend using a volt ohm meter for these tests. I do not recommend using A TEST LIGHT due to the fact that you will be testing a circuit that is wired to the air ride control module, and there is a possibility of you damaging the module with a test light !!! I have been there, done that, NOT GOOD.
Ok with that said: your wire colors should be as follows:
one that's( gray and red)
another that's (light green and red)
another that's (dark blue and yellow)
and one that (light blue and pink).
Disconnect the connector at the relay and you'll be testing the wires in the connector (THAT HOOK UP TO THE RELAY). The air ride compressor and the air ride solid state relay share the same ground which is the light green and red wire.
Turn your volt ohm meter to dc volts scale and attach the black wire (NEGATIVE) lead of the volt ohm meter to the light green and red wire.
Hook the red lead of the volt ohm meter to the light blue and pink wire.
Here your volt meter should read battery voltage (of your car's battery) if not check the (F2-111) 50 amp designated fuse in the fuse box under the the dash on the passengers side (KICK PANEL).
If this fuse is ok, make sure you were making good contact with your test leads into the compressor relay connector.
If you're comfortable with the fact that you have a good connection at the relay connector and your fuse tested ok, then you have a ground problem at ground point G101 which is located right near the mounting location of the air ride relay.
If you had battery voltage when you tested between the (light green and red) and the light blue and pink wires, you have confirmed the power source and ground to the relay.
I should clarify myself at this point. The wires at the relay are as such: The ground is the light green and red wire, the light blue and pink is the fused power source to the relay, the dark blue and yellow wire is the relay trigger source from the air ride module to the air ride relay, and the grey and red is the relay output (battery +) to turn on the compressor. OK.
So now we're down to checking the trigger source to the relay and the relay output. At this point I want you to re-hook up the volt ohm meter with the meter still set at volts d/c scale and reconnect the (red lead) of the volt ohm meter to the (light blue and pink wire) and connect the (black) lead of the volt ohm meter to the dark blue and yellow wire (again at the relay connector).
Now this next step is best done with the help of an assistant!!
While watching your volt ohm meter, have your assistant turn on the key and open and close the drivers door two -to- three times. After cycling the door, you for a short time should see at least 5 volts minimum, if not battery voltage at your meter.
(this is a little bit unclear to me due to the fact the air ride module shows that the dark blue and yellow wire, as a ground from the air ride module to the relay. but does not clarify exactly what value that ground signal should be). I am referencing Fords own wiring diagram.
A solid state relay usally is allowed a trigger source of a lower voltage then a standard relay. If you find you have no voltage reading at your volt ohm on this test, you'll first want to check fuses F2-20 which is a 30 amp fuse and F2-27 which is a 5 amp fuse in the same fuse box as the F2-111 fuse you checked earlier.
The last test you need to make at the relay is checking the relay output to the compressor. This will be done by again using the volt ohm meter. This time you'll want to hook the black lead of the volt ohm meter to the light green and red wire at the reay connector and hook the red lead of the volt ohm meter to the grey and red wire at the relay connector. Again for this test, you'll need to have a assistant turn on the key, then recycle the drivers door again.
If the relay is working properly you should have battery voltage, aproximately 12 volts showing on your meter. If not and all other test procedures results were correct, you have a bad relay.
If you have 12 volts on this test we have confirmed the relay is good and the trigger signal from the air ride module is operating as designed.
If the pump runs like you said (when it is straight wired ) the remaining possiblity is a broke wire between the air ride relay to the air ride pump (this being the grey and red wire) which you can test by switching the volt ohm meter to the ohms scale and touching one lead of the meter to the grey and red wire at the relay connector and the other to the grey and red wire at the compressor (with the compressor and the relay both disconnected). Your reading here should be 0.5 ohms or less. If you have under 1.0 ohms you're ok but specs are 0. 5 or less.
If you have an auto ranging type ohm meter, be sure your reading in ohms and not kilo ohms or mega ohms.
If you find while performing the test from the air ride module to the air ride relay (dark blue and yellow wire) referenced as the trigger signal, incorrect and all fuses all checked o.k. then it is possible the air ride control module is defective. But, before condemning the module, there are a multitude of input signal;s to the module that would have to be checked.
WARNING: Make sure your tests are accurate. Good to check and re-check each test. Be confident of your results.
Inaccurate tests and inaccurate test results= unnecessary parts replacement. Results are large dollars spent when unneeded.
Hope this helps you out.thanks for using fixya

Is the air suspension switch in the rear turned on? if the height sensor on the rear axle is bad or disconnected the system doesn't know its low.

Recheck the fuses of navigator..usually they are the only reason for such kinda issues... or else get it checked by a mechanic.