It's because in this case it's technically being used as a particle. Literally 'こんにちは' translates to 'This day' but it's used as 'hello'. All subjects are marked by はbut pronounced "wa". Just keep in mind if you see はafter the subject of the sentence it will be pronounced as "wa".

Georgia is absolutely right. In the old orthography, which had been used until the end of the pacific war, we used は to represent the "wa" sound except at the top of a word. After the war, the orthography was reformed and は became limited only to be used for the "ha" sound with the except ion of particles. は in こんにちは and こんばんは stems from a particle, so it remains to be written as は with the "wa" sound.