Time for the Weapons Expert (and avid SW reader) to step forward...
First, Nowhere is there any indication of ranges for the weapons on the Super Star Destroyer's weapons. Nor is there any set hitting power equivelent for them. What I DO know from reading the Star Wars books is that warships are more than capable of engagingin planetary bombardments from orbit.
The Phoenix destroyed a Frieghter at a great range, but...Starfleet ships, as we've seen, do most of their fighting in close. Visual indications during the battle of the Baisan Rift in Nemesis would suggest effective fighting ranges of between 1 kilometer (considered Point Blank range for large warships) out to about 100 Kilometers. Also, directed energy weapons rely on focusing the energy beam very tightly. As range increases, power decreases. While a shot at extreme range may destroy a frieghter, chances are power bleed off is so bad at that range that effective fire against a warship is probably useless.
A Super Star Destroyer is generally accepted to be 11,000 meters long, and armed with 250 turbolaser cannons, 250 heavy turbolaser cannons, 250 Ion cannons, and 250 cuncussion missile tubes. The Enterprise E is 685 meters long, and is armed with not less than 14 phaser arrays and 6 torpedo tubes. the Enterprise E is relatively meneuverable, given it's size, but she's not exactly a fighter jet, either.
Someone mentioned the A-Wings...the attack by the A-Wings that took down the bridge deflector shields was late in the battle, after Ackbar ordered the fleet to assault it. We have to assume, then, that the Executor was under attack by numerous well-armed cruisers. That kind of fire from multiple angles would strain the shields in such a way that the A-wings might be able to knock out the bridge Deflectors.
So, now, let's assume that the two ships did meet in battle, and actually fought. Most sensible Captains would run from a ship more than 11 times your size and armed as well as this thing is, but lets say you've got Captain Crazy running the ship. or me.
the Soveriegn class starship opens by firing opening shots at maximum range. at this range, both ships are relatively small targets, but the Enterprise lands a few hits. at that range, the effectiveness and slow rate of fire for the main phasers means little effectiveness. gotta close with the ship to do real damage. So the Captain closes....
The Enterprise enters ideal firing range, and opens fire with phasers and torpedoes. Problem is, at this range, she's also vulnerable to the fire from the Destroyer. the Destroyer's Captain, unsure of the effect of Ion Cannons against this odd vessel, powers down most of them (keeping a few open for test-shots) and redirects power to shields. While the Enterprise was closing, though, he deployed his fighters, and has them waiting. he brings online his turbolasers and heavy turbolasers, and the cuncussion missile tubes. the Enterprise again fires first. It's Phasers and torpedoes rake the Destroyer's now reinforced shields. the Destroyer's Captain rolls his ship to present an Edge-On profile to the Enterprise (the narrowest profile for the ship) which also brings to bear roughly half of his weapons at this range. the return fire from between 100 and 200 guns, plus missiles, is enormous. the Enterprise is constantly rocked by shield hits. Turbolaser and concussion missile fire bleed off the ship's shields, but Enterprise presses the attack. She slashes over the massive ship's hull, firing downward. the return fire damages the ventral shields, and as Enterprise comes about, the fighters jump. 144 TIE Fighters, Bombers, and Interceptors swarm the ship. while the fighter's weapons aren't individually a serious threat, used in a massive attack, they quickly begin to cause shield damage. TIE Bombers swoop in firing their cuncussion missiles, while TIE Fighters and Interceptors make strafing runs at break-neck speeds. Enterprise is now overwhelmed. While her weapons may have given her a decent chance, against more than 100 individual firing platforms, the ship is overwhelmed. Combat Coordination between the fighters and the Destroyer keeps the Enterprise under constant fire, while she returns fire ineffectively with weapons designed to fight against other large ships.
in the end, the Destroyer and it's fighters prove too much. With 750 weapons and over 140 fighters, the Enterprise's shields fail. the Fighters target the weapons systems and other key distinguishable targets, making hit and fade attacks, while the Destroyer rakes the ship with punishing solvos from her main battery guns. Cuncussion Missiles rip open the engineering hull, and turbolaser fire causes the warp core to breach.