Very likley the micro switch that is activated when you step on the brake pedal is either bad or out of position. This the first step in the system for the automatic shift lever to move. It is a safety mechanism that keeps kids from shifting out of park since they probably cannot reach the brake pedal in the sequence. The manual over-ride bypasses this system to allow service tech to work on the system without having to press the brake pedal. The micro switch is located above the brake pedal and is part of the brake pedal linkage. Usually this is the problem. A fairly simple thing to diagnose

These people seem to have had a similar problem: http://www.cargurus.com/Cars/Discussion-d976_ds40422
http://answers.yahoo.com/question/index?qid=20060817071715AA0NlFO
The consensus seems to be that it's an issue with the brake light switch. Perhaps you should look into that? If you do, then the following might help:
"It's likely either a bad brake light switch, or a blown fuse. Both are pretty easy fixes. The brake light switch is located under the dash and is in some way directly- usually above it- connected to the brake pedal.
(There may be 2 switches- some cars have a switch for the main brake lights as well as one for the high-level third brake light. Have a friend look at the rear of your car while you step on the brake to make sure.)
DISCONNECT the switch and check it with an Ohm meter. If you don't have one you can get a decent one at Radio Shack for less than $20."

There may be a problem with valves or solenoids used to automatically shift your transmission into the proper gears. By selecting manual override, you allow your computer to ignore faulty valves/solenoids while you take control yourself.

Usually your computer can warn you about such problems. Look at your dashboard and see if a yellow engine icon light appears to be lit when your car is on running idle. If so, you should go to your nearest local auto parts store and borrow/buy an On Board Diagnostic scanner (OBD II).

On OBD II device will allow you to connect the cable to a port underneath your driver's side dashboard and read the Diagnostic Error Code related to your engine light warning.

See if you can find your error code from this list:
http://www.hondacivicrepairs.com/mil_cel_codes.asp?q=Trouble%20Codes%20(MIL%20/%20CEL)%20-%20Honda%20Civic&id=23

Then learn more about your error code so you will have a better understanding of what needs to be fixed when you bring your car to a shop or dealer. The idea is to educate yourself about your issue at minimum so you are not scammed into paying for repairing problems that really weren't problems to begin with.

Good luck!

If you're talking about a problem getting the car out of park and into gear, that's a vacuum switch that your dealer should be able to fix. Over time these can get gummed up (either from dust or from debris - something spilled onto the shift). Just bring it to your dealer. Should be a ten-minute job to either open up the shifter housing from above and blow out the debris with compressed air. Or a replacement is pretty simple too. Less than $50 I believe. Good luck.