Afraid of heights? maybe.
Fire villains, are pretty obvious. Von nebulas gang are as well, being crushed, toxins, explosions. ETC.
The Savage planet villains can be seen in that light as well, people being afraid of wild animals, even without knowing their true intent. and fear of being controlled by the power hungry.
Breakout has some as well, Jawblade is a shark, so the fear is obvious. Toxic reapa, once again, toxins. Thornraxx is fear of bugs. Splitface could be serious mental disorders. Black Phantom could be fear of someone looming in the dark, pulling the strings that make the world tick. (Think Illuminati stuff) Core hunter is pretty easy, serial killers. Speeda demon could be drunk/unsafe drivers. Voltix could be fear of electric shock or maybe even power outage/EMP. XT4 could be fear of work equipment, such as saws, jackhammers and all that.
Brain attack seems to maybe continue and rehash a few of these as well. Invasion from below I guess is just fear of the unknown, and misunderstandings that lead to more problems.