Always upgrading the small protector to use as speed up/siege ships, otherwise It is only medium hunters

For most factions (Riftborn are the main exception), three upgraded Attackers will do at least 50% more damage than an unupgraded Hunter while also having more hp, more hp from shield modules, probably more effective flak and comprable benefits from non-squadron support modules. Still ignoring squadrons, the Protector/Coordinator comparison is if anything even more skewed in favor of the smaller ships, given how much more movement you can get out of fleet-wide engine modules with them. There are advantages to medium hulls, namely less strategic resource use, slower attrition, the ability to upgrade into better designs in the next ring and access to squadrons, but if you need the most power for your CP right now, small ships are the way to go.

Interesting. I always thought one medium ship was better than  some upgraded attackers. My main Riftborn strategy is to mix Riftborn medium ships whit defenders, upgrade them, and grant riftborn medium ships about 16 movement speed whit fleet movement bonueses from defenders. 4 Defenders in a riftborn fleet gives simply so much speed that its crazy, neither sophons can get faster than that. Plus i get much more attack and defense than most other fleets in game... making a single riftborn fleet, seriously OP.

I wonder if there is an alternate strategy early game for riftborn besides that?

Can i even use riftborn small ships effectively? I never tried it, tro be honest... Instead of going for 10 movement speed attacker ships, i simply go straight for OP medium ships and buff them whit insane speed whit defenders. Seems like the best choice, eh? 

I tried it once against the AI in endless difficulty and he was seriously hopeless lol

In the last game where I did anything military with the Riftborn, I built a bunch of small hulls without modules (mostly Attackers) in my border systems and then upgraded them as needed. Having them right where I needed them let me skimp on engines and Protector support. Your strategy might be the strongest any time that you're warring in the mid-game, though: Riftborn are the exception to the rules of small/medium hull balance just because their Hunters can mount so many weapons.

My favorite use of protector ships is as ferries.  Two or three loaded with H-field accelerators will scoot your fleets around in a hurry.  If you manage to find A-M accelerators, even better.  When Q-fields hit, you'll feel like the Vaulters.

"Oh.  Look.  Someone's sieging my system and my fleets are on the other end of the galaxy."  ZOOOOOOOOOOOOOOOOOOM "aaaand now I have three carriers in their face."

The main advantage of small ships is that they're cheap in terms of production, upkeep and strategics; they're quick to produce and get you more total module slots (for the most part) than a CP-equivalent fleet of bigger ships, especially with upgraded hulls.  Because you can vomit out fleets of little ships, they're great for patrolling, providing sight, causing distractions just threatening enough to answer and fighting fires while your main battle fleet goes after an objective.

Some modules get multiplied effects on bigger hulls, but if they're not the purpose of the ship in question, then it's a win-win.