I think a lot of the issues come back to the two very different ways of playing.
To someone roleplaying a pirate it's blindingly obvious that they attack targets of opportunity who are unprepared (and often unwilling - though of course without a flag there is no way of signalling this).
Whereas others are not roleplaying anything - they are just playing a game hoping to bump into like minded people and the idea of finding themselves outgunned and outnumbered forced to comply, flee or blow up doesn't strike them as fun for them.
Not just that. There have been academic articles on the kinds of players that engage in MMOs and other similar games, and how they interact; most kinds of player tend to interact well, making the game richer and more enjoyable for everyone involved, but a specific kind that sits somewhere between PvPers, PKers, and griefers have the opposite effect, making the game worse for others and driving them away.
(Not saying that PvPers and PKers forcibly are like that, just the ones that don't mind when they cause grief to their targets.)
It's what led to a particular definition of griefing being coined by MMO devs, and used as a guideline in more than a few games, starting with UO:
"A griefer is someone who, through his social actions, costs you more money than he gives you." It doesn't matter that the griefer is operating fully within the rules, he is still bad to the bottom line of the game. Ever wondered why after Ultima Online almost every MMO put much stricter restrictions on how players could negatively influence one another, removing things like player looting, restricting where and against who the players could PvP, and so on? It's the effect of numerous devs that worked in UO, and saw the game almost close down due to out of control PK activity, going to work in about every big budget MMO being made.
In ED the effect is somewhat different because of the modes. Instead of leaving, players go into Solo instead. It's just as bad for those whose play style depends on having targets, but not as bad for Frontier because the player is still playing, at least for the time being.
One thing CQC seems to be showing is that quite a few people who shun open PVP seem to be quite up for CQC PVP
Naturally. PvP isn't just one monolithic thing, there are many kinds of PvP, just like there are many kinds of PvE. CQC makes PvP on demand (matchmaking), removes the penalty for defeat, provide a far more even playing field than Open could ever hope to, and guarantees that the opponents are willing to fight; it's a completely different beast, far closer to a LoL or TF2 match than to fighting other players in Open, which means it attracts the large potential player base that loves Arena PvP but isn't interested in a virtual world with PvP included.