The Fire Elemental would take more damage.

The water elemental is not immune or resistant to fire damage. This would indicate that the fire elemental's fire form ability would damage the water elemental. The fire form ability can inflict damage in 2 different ways:

1. A creature that touches the elemental or hits it with a melee attack while within 5 feet of it takes 5 (1d10) fire damage.

This would indicate the water elemental would take 1d10 damage if it enters the fire elemental's space, because they would be touching.

2. When the fire elemental enters a hostile creature's space and stops there, the fire form ability has three separate parts:
   • the creature takes 5 (1d10) fire damage.
   • the creature catches fire
   • until someone takes an action to douse the fire, the creature takes 5 (1d10) fire damage at the start of each of its turns.

In #2 the first part is separate from the second two parts. There is no indication that catching fire causes the initial damage, it is presumably high levels of heat. However there is very clear indication that catching fire causes the additional damage on new turns (until someone takes an action to douse the fire...). And because it indicates that it can simply be doused, we can safely presume that it is non-magical fire that will be immediately doused by the water elemental's form.

So the water elemental would take the initial damage, but none thereafter.

However the water susceptibility trait of the fire elemental would also cause the fire elemental to take damage.

Water Susceptibility. For every 5 feet the elemental moves in water, or for every gallon of water splashed on it, it takes 1 cold damage.

In both cases above the two elementals are in the same space and touching, and I would consider that the same as splashing. It would be up to the DM to determine how much damage the fire elemental takes, but it would seem to me that it would be a lot more damage than the fire elemental would cause to the water elemental. A water elemental is listed as Large and I would guess made of at least 100 gallons, that's up to 100 hp damage to the fire elemental. The fire elemental wouldn't get all that damage, maybe 1 - 3 d10 depending on the situation.

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.