I have charged my battery by connecting to the terminal under the hood scores of times over the past 10 years and never had any issues. I always have the ignition off and the key removed. I have never seen it draw more than 10A from my 15A charger even with a battery low enough that it won't start the engine. I have even inadvertently set the charger switch to 100A start position which pegged the ammeter with no problems.
My guess is that the transients (sparks) that occur when the charger cables are connected and disconnected somehow got into the electronics that were connected with the ignition switch in the on position. Most good electronic designs have transient protection built in so these protection devices may have did their job and clamped the transient and the resultant current surge just caused a fuse to blow so the electronics were protected. I agree that you should check all the fuses.