Whenever the gamerule mobGriefing is set to true, then the EnderDragon is capable of destroying Command Blocks just by flying through them.
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Withers are unable to destroy command blocks. Also, Mojang staff fixed a similar bug where the Ender Dragon destroyed barrier blocks. See MC-46591.
Fair point but it wouldn't make a difference since any red stone hooked up to the command block can be destroyed. Blocks that avoid Dragon destruction have purpose if they are for structures. I fail to see how changing this would benefit anyone. Of course you have the mobGriefing rule if need be.
Every change breaks someone's workflow. Command blocks can only be acquired or edited with cheats or op privileges, and can only be broken by players in creative. It's not unreasonable for the player who placed it to expect that it won't be broken accidentally. They're also more work to set up than most blocks because of entering the commands. Either way, it should be possible to fix automatically using some testforblocks and clone. And if you were actually relying on the Ender Dragon breaking a command block... well, aside from that being strange, the same argument applies: the redstone hooked up to the command block can be destroyed, and you should be able to use that for whatever you were relying on the Ender Dragon breaking command blocks for.
Torabi, command blocks are impervious to dragon attacks now...
I actually was relying on the dragon to break command blocks. I know. It's strange... It makes sense if you knew what I was trying to do but I can't go into details because it's for my map (hush hush you know). But I'm sad. Oh well. It is what it is.
@qmagnet
If you were using command blocks, you would know that you can check if there is a dragon within a radius, and if there is, the command block will do something, you can even make it destroy itself with a setblock command.
Works as Intended.
"The Ender Dragon will destroy any block it comes into contact with, except Obsidian, End Stone, and Bedrock."
http://minecraft.gamepedia.com/Ender_Dragon