The only honda's that this affects (to my knowledge) are the 96-98 Civics. Honda had the infinite wisdom to integrate part of the factory keyless entry into the factory headunit...once again Honda gives us the shaft.
It's very easy to fix this problem though....all you have to do, is keep the factory head hooked up, and stash it somewhere. I'm not sure if Metra or one of the other companies makes a specific harness for this application, but with a helms manual and some splicing you can easlily get this one to work.
This web site has the whole install documented for you, including how to work around Honda being a moron when it comes to their audio integration:
http://www.installdr.com/InstallDocs...PDF/466013.pdf