Monster Warriors (2006) seems to fit pretty well... Apart from it being live-action, and not a cartoon (though the awful CGI is cartoonish).
The National Library of Australia covers the "giant" part:
What's going on in Capital City? Major monster trouble is what is going on. An earthworm so enormous it's eating trains, a giant squid that's munching whole fishing boats, a giant ice monster who can freeze you with one breath.
And Wikipedia covers the "mad scientist" part:
The series, a purposely campy cross between the Power Rangers and Ghostbusters, follows the adventures of four teenagers fighting to safeguard Capital City from the vengeful wrath of insane and disgruntled old B-Movie director Klaus Von Steinhauer who possesses the ability to bring his cinematic monsters to life ("I make ze monsters big!"). Over the course of the series, various story arcs occur that expand the series cast and city locations. Each week sees the teens customize common household objects into useful weapons to fight against monstrous creations.
- big monsters, created by a mad scientist-type guy (check out the first shot of the opening below)
- monsters come in various tastes, but the episodes list has its share of insects, with a carnivorous butterfly, bumblebees, termites, stinkbugs...
- the monsters are fought by teenagers
- title resembles Monster Hunters, aired after 2000
- it's not a cartoon... But, what passes for "special effects" is so bad it's borderline cartoonish (see these stinkbugs)
Remembered from TV series with a Team which I recalled was IDed as "Monster something".