I'm usually pretty open minded when they try these shake ups in the comic books, knowing that eventually things will go back to normal. I've seen nearly every hero die, then come back, be mind controlled, or have their body taken over by a villain....and eventually things go back. That being said, this one just doesn't sit right with me. There is a good article over at Newsarama, "Why can't they just let Captain America be Captain America", basically detailing how since he was "killed" after Civil War he has been lost in time, then in another dimension, then aged, then depowered, and now this. It seems to work well with the movies having Cap be the All-American leader, who always does the right thing...the comics seem to shy away from that. This twist, and they said there is no doppelgänger, mind control, etc. to this, fundamentally changes the character. Hopefully things will work out, it's only one issue, but this is one change I'm not a fan of.
As far as Marvel's situation, they haven't ever really done a "reboot". They start over at new number ones, nearly yearly, but the previous stories and history are still in tact. They almost run the books like tv in a way, with a new "season" each year. I guess this keeps the history for older readers, while offering an easy entry point for new readers. I think they think an "issue 542" might scare some people off. DCs New 52 initiative that is just wrapping up now, was more of a reboot that started a new history, which they seem to be course correcting a bit now by bringing back stuff from prior to that. Hopefully it works, because I had dropped down to basically 3 books now from DC as the rest seemed unfamiliar or dark for dark's sake.