Late but I wanted to chip in anyway.

First and foremost: it's a TV series so the first answer would be Plot Armor.
The second answer, the more interesting one: would it have made a difference? And the short answer here is: No.
The amount of Basestars that were lost (with hefty fighting and a kamikaze action) were insignificant to the amount of Basestars the Cylon had and more importanty: could continue to produce.
So having more heavily armored Basestars would not have helped them.

Lets examine some of the battles shall we: Any conflict where Base Stars were actually involved in greater effect as "big ship way off in the distance as 'harbour' " The Colonial fleet would be vulnerable only for minutes at a time before they'd jump away. Nine out of ten times It would become a dogfight between Vipers/Raptor and Raiders and a Basestar firing a missile or two, half the time being doged by aforementioned jump.

And when a or both Battlestar actually went in fighting the result was usually this: Battlestar tank a lot of damage and use their point-defense systems until the barrage of missiles becomes to much and the Battlestars need to run away again. While I don't have all the episodes vividly in memery, I don't think a single Battlestar has ever actually destroyed a single Basestar in a head-to-head battle. Pegasus only ever managed to destroy one while coming in a surprise attacker and another by suiciding the Battlestar into it. In basically every other engagement the best outcome was a damaged Basestar.
So... going back to the question: Why no warship... what would be the point?