What am i getting at you'll ask?
Well, if anybody should be feeling bad about flying axis it should be Greeks
Despite all that, i have no problem flying on the Axis team. I fly sims to experience a specific part of history that i like, so that i can further understand and study it. I don't feel guilty at all. If anything, i get an even better appreciation of what our grandpas did back then when i see how superior the 109Fs they faced over El Alamein were against their Hurricane Mk.IICs, or how outclassed their PZL24s would have been against an onslaught of 109Es during that April of '41.
There are a few other posters on this board that i know to be Greek and they also mostly fly axis aircraft. Heck, i was flying blue on IL2:1946 mod maps that had me flying over a scaled down depiction of Greece and i still had no apprehensions about it.
That being said, it doesn't mean it's the same for everyone. Some people will get a more emotional response, so understandably it will be harder for them to fly on the "enemy" team.
By the way, i think it was Krupi on these boards who once commented about a scheduled multiplayer event when the time was adjusted to allow US players an easier participation: "Damn Yanks telling me when i can bomb my homeland, what's next?". I hadn't laughed that hard in quite a while
For me the answer is simple. Each one should fly what they are comfortable with, understand there is no shame in that and finally, realize that other players might have a different feeling about it all and not judge them negatively. We're here to learn, appreciate the efforts of people on all sides and have fun while doing it, not relive the hatred that caused that mess in the first place
