Not Updated For Current Season
The masteries shown here are not yet updated for the current season, the guide author needs to set up the new masteries. As such, they will be different than the masteries you see in-game.
The reason for the skills maxing rune prison first is simply for the 6 ticks you acquire at max level dealing great damage. After the main prisoning sequence you want to do Ryze's main source of damage, overload. Overload late game with an amazing ability build and magic penetration will deal great damage. Then lastly spell flux comes into play, the main go getter for double and triple killing enemies. Using Ryze's ult is very important during the hairy situations dealing with multiple enemies, where once ult'd ryze gains an extra AOE damage on all skills he proceeds to use after his ult, meaning loads of high, fast damage.
The runes I would use for Ryze is strictly built upon the basis of either ability power, or just an all out spell penetration for that extra bit of damage.
Ryze, one of the strongest, easiest, and just one of the nukiest character in League of Legends. Ryze is great early game, as well as late game, great for starters, and just overall fun if you enjoy devastating entire teams with Ryze's overly powered skill combo.