In short, we think 1 keypress = 1 symbol printed on the screen. That explicitness brings peace. But, we also think that ligatures are optional and many people like them (read about all the pros and cons in the link above).
You are not alone. While I can imagine a feasible use for some very commonly used glyph combinations being made a ligature, I just really prefer the one glyph per key press presentation (kerning them well OTOH is always greatly appreciated). Unicode in text editors still bugs me in that way, in the back of my mind I know that pretty non-ASCII character is taking up more than a byte, and it's... distracting.