The main reason is the same reason why CIWS are not used on ground vehicles - anything smaller than a ship just doesn't have enough space/weight allowance to fit one, let alone two. The lightest CIWS I found, an outdated version of Soviet AK-630 system, weighs in at 1 ton (later versions are much heavier), has a turret ring 1m across, is 1 meter high above deck and needs 2m of space below (which means that installing one would also going to be aerodynamically awkward) - and all of this does not include the ammo supply (2000 shells for this version translate to additional 0.2 tons, later versions, again, had more ammo). All modern CIWS weigh at least 6 tons, are considerably bigger, and some of them also need an external targeting radar - and I assume not all bombers have the equipment needed by default. Aircraft also has more approach vectors to cover - a ship only needs CIWS installed on top, but a bomber would also need defence in the lower hemisphere; so for complete coverage we would need even more guns, which would mean even less speed and payload.
Even if we would manage to fit some in - gun-type CIWS effectiveness is disputed. Their limited range means that even a succesfull kill on an incoming missile might not protect the ship from an impact - and what would be a minor inconvenience for a warship, will be a deathblow to an aircraft. Missile-based defences are usually considered a better choice, as they can engage and destroy incoming missiles at significant range from the protected object - but they are even heavier and bulkier than guns.
And last, but not least - modern strategic bombers tend to eschew defensive armaments at all, because their main weapons are missile-based, and imply a launch at safe distance from the enemy.
Thus - modern CIWS on a bomber are impractical. They are heavy, bulky and do not provide immunity to missiles, so might as well stay on the ground.
P.S. On a closer inspection, several other bombers had or have radar-controlled tail guns - Tu-95 or early B-52, for example. B-52's tail turrets were removed after a friendly-fire incident where radar-homing HARM missile locked onto the gun's targeting radar - another downside that I haven't noticed before.