1) EFFICIENCY. A single missile or heavy cannon blast from a large capital ship can deal enough damage to completely vaporize a small craft like a fighter instantly. This isn't an old Final Fantasy game though, and the fighters aren't lining up to be shot. Fighters with 3:1 thrust ratios and above can be extremely hard to hit when they stay moving. AI turrets don't track them well, and even most missiles have trouble catching up to them (with overdrive you can outrun any missile). So they can survive for extended periods in the face of extremely heavy firepower through simple evasion, and a nice side effect is that they sometimes draw heavy fire away from other ships. Add a jump drive to your fighter, and it directly impacts the fighter's primary survival strategy. Because it's not just the weight and size of the jump modules, but they require more energy, so the power system needs to be expanded. If your fighter is armored, the armor must now be extended to cover the jump modules and additional power, and as a result, additional thrust must now be added, which also requires more power. Even if you add enough to bring your thrust ration back up above 2:1 or 3:1, you've now made your fighter a substantially larger and easier to hit target. Try this: drop a core with 1 power, 2 engines, a radar jammer, an overdrive comp, and 1 overdrive module. Get in and fly right up to a pissed off enemy base with turrets and then see how long you can dance around it without ever taking a hit. Now try that trick in a 1.5K mass armored jump "fighter."
2) ECONOMY. Fighters are meant to be rather expendable and overwhelm the enemy with numbers and too many targets to control. This means if you include fighters in your fleet, you are probably expecting losses anywhere from 25-100% of them depending on how things go. Considering this, how wise is it to throw away expensive jump modules and more than minimum armor and shields on them when you know you'll lose some? The alternative is to have all the extra systems (jump, inhibit, scan) on your carrier that can escape if a fight starts to turn South. Keeping the front line troops as cheap and simple as possible saves you lots of resources in the long run, so you can actually lose a battle and still fight the war.
A fun trick I worked out recently is an extra light carrier with fast jump and permacloak capability when nothing is docked to it. I jump it in with a full fighter load, deploy the fleet then instantly cloak. Then, from the relative safety of stealth I can order the fleet to attack and charge my jump drive to get away if things go wrong. If it's going well I can remain to observe and uncloak periodically to support my fighters by taking down small enemy craft with light missiles when it seems safe to do so.