Because they station was threatened with destruction only a handful of times in seven seasons, which was helped by the fact that for most of the show it was a heavily armed space fortress which fried ships that could have and in one case owned a Galaxy-class.
But remember, it's fiction, so who wins or loses an engagement is determined by dramatic necessity. The hero ship will always survive things that will destroy a guest ship of the same class. So that kind of ranking of relative strengths doesn't really hold up.
In principle, the E-D was just as heavily armed as DS9 was. In fact, it was more
heavily armed than DS9 was in seasons 1-3. The ship was specifically designed to be as safe as possible for its inhabitants, which is why a ship that was intended as a research vessel had such massive phaser strips all around the top and bottom of the saucer. The ship wasn't meant to get into fights, but its designers made sure that if it did, it would be able to protect the people within. That was fundamental to the design philosophy.
The problem, again, is that the rules of fiction trump the rules of common sense. Dramatic tension required making the ship seem more vulnerable than it realistically would've been. In countless ways, good safety design was ignored in order to make things as perilous as possible -- there were no seatbelts, security had no armor, holodeck safeties could be deactivated, and systems that should've had multiply redundant safeguards didn't have them. I mean, come on, fiction requires putting characters in danger, so even if the series had been set at Starfleet Headquarters, you can bet that San Francisco would've become the most dangerous city on Earth. (How many times has New York City been trashed in the Marvel Universe? How many times has London been invaded in Doctor Who
? Yet people still live there and raise families there, in real life and in fiction.)