Sounds like you are using a standard wallwart charger that will charge your transmitter and receiver at the same time.
Several things to look at.
1. make sure your switch on your plane is turned off when charging and make sure your switch is hooked up right. (most switches have the single lead going to the receiver and the spare lead where there are 2 wires coming out of the switch is for charging)
2. Make sure it is a dead battery and not a problem with comunication with your transmitter (crystals fully seated, antenna routing ect...)
3. Use a loaded voltmeter or voltwatch to check your battery, something you should do before every flight anyway.
4. it may be possible you have a bad charger or battery but check everything else first.