Originally, the word derives from the greeting: 「今日は（こんにちは）、ご機嫌（ごきげん）いかがですか。」 *It means 'How are you today?' And, as time passes, the greeting has been shortened, it became just the word: 「こんにちは」 So, in the word, 'は' is a particle. It's pronounced 'wa'. 'こんばんは' has the same derivation:)

A couple of reasons, mainly because this is the particle は (wa) rather than the character は(ha). Second, 「こんにち」 quite literally means "this day" or "today". In terms of how the は particle works, this is kinda like saying "about this day" or "under the circumstances of this day", similar to how we say "good day". Although we simply imply that we want things to be under the circumstances of a "good day", the Japanese usually like to end thing in particles, so they don't imply the 'circumstantial' bit and thus use は. As you learn more about the は particle this will make more sense.