I was playing the Advent and the enemy was the Visari.Wouldn't MORE capital ships be a good thing?
Not necessarily.
It sounds like the enemy had a lot more frigates than you, so even though you had more caps, he had a much higher damage output.
Cap ships have a fairly low ratio of 'firepower to cost', both in terms of the resources required to build them and the amount of fleet capacity they use. In general, 50 fleet capacity of frigates will have a much higher combined DPS than a single cap.
Essentially, it's about balanced fleet composition - no Cap ships and you lack the powerful abilities and durability that they provide, too many Cap ships and you lack the firepower that the smaller ships provide.
Of course, working out the right mix of cap ships and frigates is the tricky part, especially as it changes with the situation and the opponent.