What do you mean, the real reason?
I'd have thought commercial reasons would be the real reason... Athough it covers a whole host of possibilities you're unlikey to find out the exact soecifuc thinking behind the change. They have a limited number if aircraft and if the aircraft that operates the SOU-FRA route can make more money deployed elsewhere then of course that is the right thing for BE to do.
With regard to AMS I doubt that will get the chop anytime soon as they've just started a code share agreement with KLM and the route is 3x daily.
It's also worth noting that Flybe have pulled out of FRA altogether now after dropping the long running MAN and BHX connections last year. Clearly Flybe don't see much success at FRA these days so are moving the aircraft to better money making routes.