First, .htaccess files along with any other hidden files (starting with a period, ".") do not show on most FTP programs. If you have an option in your FTP client to show it, it will be somewhere under its general settings as was said already. The best way to see/edit/remove it is under telnet.
In Windows, open up the command line under Start Menu > All Programs > Accessories > Command Prompt then type in the following when it comes up...
(enter your username & hit enter)
(enter your password & hit enter)
You should then be able to see the .htaccess file in there. If you just want to edit the file on your computer and upload a new version, go ahead and do that like you do every other file. If you need to get rid of it, follow the above instructions and then type "rm .htaccess" and enter to remove it.
Hope that helps!