It's actually very common. If the rules aren't just suggestions, then the DM can't change any of them. Yet he can, so they are just suggested rules. Most people I've interacted with here understand that the DM can change or add rules, which makes RAW just suggested rules to follow.
That said, the overwhelming number of the "rule suggestions" are followed by DMs. There aren't many DMs who want to write a whole new game or even most of one. They just going to follow the rules 95%+ of the time and make some house rules for the remaining few percentage points.
They also are not doing it on whims or unfairly pretending to follow them.