Rather more to it than that
Starting with a clean sheet design you choose a target and and then see if you meet all the rules.
under JAA/CS there are the obvious handling and control margin ones, the roll authority and flutter demo ones generally handles the blade stall issue. One of the first things to do is see if the selected value is sensible and achievable (i.e are the loads OK to produce a usable fatigue life and to have adequate strength margins,, is the vibration tolerable, is there sufficient power margin to make the value usable? There is no point in being in a 2000 fpm ROD at Vne.)
Part of the original decision is structural strength to cover air loads and bird strike requirements, UK military rules base the operating speed (Vno, which is equivalent to civil Vne) as 0.9 x Vne, where Vne is 0.9 x max demonstrated speed, so a UK design demonstrates 123% of the operating speed, civil rules is 111%.
there is never just 1 reason why Vne is what it is.....HOWEVER NEVER EXCEED IT AS YOU HAVE NO IDEA WHAT SET IT AND SOMETHING YOU HAVEN'T CONSIDERED MIGHT BITE YOU, THE CLUE IS IN THE NAME.....NEVER EXCEED SPEED
DM