It all depends on the server that is running factions and how they use it. Factions as a base plugin is easily abused, which why you should play on a server that knows the limitations and effects of the plugin as well as how to config it.
So when you get on a server and are killed by super diamond people or are griefed, that is the fault of how the owner(s) configured the server. It could also be that the admins/mods are really balanced as sell a server as "Pay to Win" so the people who actually donate get access to full diamond everything with super enchants, which isn't a very good approach to getting new players.
The way I use factions is to make it so players can't break blocks in faction territory, but then be able to open chests and wooden doors, so you have to design your base to keep them out (also I had explosions on, so you would have to design a base to be resistant to tnt cannons and creeper herding!) Also, I added a economic cost to creating factions as well as declaring war. The map also doesn't show neutral factions, only enemy and allies, so you can essentially hide your base. One thing, however, is letting people use dynmap as an attack catalog since people allow it to show faction claims, which is just dumb to degree that there has to be fog of war.
Factionsplus also adds some awesome features to factions that allows for increased control over power loss, for example players can get deducted more power for suicide than for pvp deaths so there's less incentive to lava suicide.
