Because Johnston's long tactical retreat, however brilliant (it is still studied in military academies), was considered to be not quite the Confederate way of doing things.
Also, Johnston had been feuding badly with President Davis since the beginning of the war, when Davis ranked him only fourth out of the five new Full Generals.
So now Davis found an excuse to sack him, and install John Hood, who seemed to display more of the Confederate spirit. But it was a diastrous decision. Hood had been moved up too high for his talents, and his gung-ho tactics in Tennessee would lead to a humiliating defeat by George Thomas - the only time a Confederate army was ever driven off in a complete rout and disintegrated.
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ANSWER Joseph Johnston was replaced two time. The first one was after he was injured during the Peninsular Campaign and replaced byt Robert E. Lee. The second one was during the Atlanta Campaign, when he was replaced by John Bell Hood.
John Bell Hood - a bad appointment that led to disaster in the Battle Of Nashville, where his army was driven off in a rout, and disintegrated.
He led the Army of Tennessee to disaster. The Confederate President, Jefferson Davis, fired Joe Johnston and replaced him with Hood, because Hood was Jefferson's idea of a good Confederate, a real gung-ho fighter and leader. (Johnston's policy of minimising his casualties because the South was running out of manpower did not strike Davis as the Confederate thing to do.) Hood turned out quite wrong as an army commander, and squandered precious lives everywhere. His defeat by George Thomas at Nashville was the only decisive rout of a Confederate army.
On the Union side, it was Sherman, aided by the popular General McPherson who was killed in the battle for Atlanta. On the Confederate side, the shrewd and cautious General Joseph E. Johnston had been replaced by the heroic but foolhardy John Hood, who managed to get his army out of the city, but then led it to disaster. Meanwhile Sherman had decided to ignore him and attack the infrastucture that supported the Confederate armies in the field. Although this was the very opposite to what Grant had planned, it turned out highly successful - reducing the enemy to starvation, while costing almost nil battle casualties. The only sizable Confederate army in Georgia was the one occupying Savannah, commanded by General Hardee. He escaped across the river into South Carolina. It is worth noting that the supposedly ruthless Sherman did not feel it necessary to destroy that gracious city before he went in pursuit of Hardee.
John Bell Hood. Jefferson Davis had fired Joe Johnston because his long tactical retreat, however brilliant, did not look like the Confederate thing to do. So he replaced him with this gung-ho character Hood, who led his army to disaster.