The battery on my 06 Road Glide was low and I heard a fuse pop and there is no power to anything. I checked the micro fuses in the box and 2 mini fuses in the battery box, nothing is blown. Any ideas?

 

Just looking at fuses will not always indicate the fuse is bad. I always check mine with a fuse tester just to be sure. Since you checked the fuses and I assuming you checked them correctly, I would say the noise you heard was not a fuse. You mentioned your battery was low and you heard a noise. You do not mention what was being done to the bike when this happened though. From this point on I'm just guessing at answers.

Since there is no power whatsoever there could be a few issues.
1. The battery is to low to provide power. May need to be charged or replaced.
2. A fuse is blown. Since it's all power I would start with the main fuse. Make sure you also check any inline fuses you have, not just the ones on the fuse panel.
3. Your starter solenoid could have fried. Could be the source of the "pop" as well. This commonly happens when you try to jump a motorcycle battery from a car battery. Especially from a running car. Using a charger not meant for motorcycle batteries could also cause problems.

I might be able to help you more specifically with more information.

 

First of all confirm that the battery is in good condition. Charge it off the bike and check the voltage across the terminals with a multimeter. It should be around 14 volts, any lower take it to a local auto parts store to get it tested. If it is dead or in need of replacement buy a new one, then charge it fully off the bike before installing it. You now have a sound basis on which to follow enodrano's advice. Let us know what you find.