Agree with JB completely. Cap was considered too much of a Boy Scout (like Superman), Reed was worked into being a cold and uncaring husband and father willing to inflict horrors on family and friends to satisfy his curiosity, Professor X became something of a monster, The Chief in DOOM PATROL became the *cause* of their "accidents," and so on.
Cyclops was only one of many to get this "feet of clay" treatment, which is flat out appalling. And it is the "too cool" writers who insisted on turning heroic figures into flawed and unlikeable non-heroes to satisfy their own inferiority complexes.
BTW, I absolutely hated the whole Emma Frost thing too. I kept expecting a reveal that she'd been manipulating him telepathically the whole time (which would be in keeping with her previous characterization, IMHO)... but no.
Seriously, screw whoever (Morrison?) came up with that bit of character assassination.
When the Scott/Emma thing first came about I thought to myself, "hmm, just trying to pull off a half-ass version of what the FF had done with Johnny and Alicia, only this one is from left field, if not outside the ball park entirely".