The scroll's effects can cover either four or nine Medium creatures, depending on how you interpret it.
Normally, effects that are described with a radius originate from a grid intersection. When the origin is defined by a creature, such as the caster of a spell, or as in this case, a creature reading a scroll, then the intersection is one of the intersections within or adjacent to that creature's space (the corner of their square for a Medium-sized creature). So if you take the "5-foot radius cylinder" as the key part of the spell, then the effect should cover four squares. One of those would be the square of the creature reading the scroll, and three of their friends could fit in the others. This is probably the best interpretation of the rule, though the description of the effect does it's best to make it more confusing by describing the effect as remaining "centered on you" as you move. Probably that just means you can pick a new corner for it each time you move.
The alternative interpretation is that the radius of the effect of a Scroll of Protection is supposed to be interpreted as a distance from the reader of the scroll, not a radius from a point in space. Since a Medium creature occupies a full 5-foot square in combat, there are 8 squares within five feet of them (forming a 3 by three grid with the creature's square in the middle). There are some spells, like the Thunderclap cantrip, that have areas of effect that work this way, and this is also how a Paladin's Aura of Protection works.
The spell Ice Knife as originally published (in the Princes of the Apocalypse adventure, and the free Elemental Evil Player's Companion that was released alongside it) used a radius to define the area of effect for its secondary explosion. But it was changed in an errata to use a distance from the targeted creature instead.
Unfortunately the exact intentions of the designers of the Scroll of Protection are not clear, so the DM of your game will need to make a ruling on how it works at your table. You could play by the strict RAW and use a radius that's centered on a corner of the reader's square. Or you could apply a similar ruling to the Ice Knife errata and change the five foot radius cylinder to a five foot range around the reader of the scroll, which might make the effect easier to understand.
I don't think either version is going to dramatically change the power level of the scroll. A larger area is not necessarily better, since you may want to be using the protection it offers to flee though a room full of the creatures you're protected from. Having a larger area means you'll have a harder time fitting through gaps in between the enemies (since you can't push the AOE against them without ending the effect). Similarly, with the larger area, the creature at the center (who read the scroll) can't easily reach the edge of its effect, and so they probably can't fight anyone outside unless they have ranged attacks or a reach weapon.