There are many reasons why planting fungus squares might be a good thing in SMAC.

In the early game playing as an eco-friendly faction like the Gaians, or using social engineering (green) so you are Planet friendly gives you a large chance of capturing native mind worms when you attack them. One early game strategy is to take your starting scout, walk through fungus until you find a mind worm, capture that worm, and then use the captured mind worm to capture another, and so on. Every combat with a new mind worm has the chance of capturing that worm, making your worm unit bigger/stronger or giving you free energy credits. If the worm gets too damaged, just set them to 'hold' for a few turns. Worms regenerate health in fungus squares.

As long as any units are captured far enough away from your cities, they are captured as 'independent' units, and don't require any mineral support. You can use these early game "free" worm units for exploration and pod popping, and also to terrify any other faction with your military might.

Native life such as mind worms treat movement through fungus squares as roads (only 1/3 movement per square), while non-native (normal) land units treat fungus as barriers (one square per turn even for fast units). The secret project 'Xenodome Project' allows you to move any and all of your land units as though fungus were roads, so once you get that you have a huge mobility advantage vs. any other faction in fungus infested areas.

In the late game, some research and secret projects make fungus squares even better than forest squares for harvesting minerals and energy. And fungus, like forest squares, makes Planet happier and less likely to retaliate with a bunch of pissed native life.

And don't forget the fun of planting fungus around an enemy city and wrecking their resource income. And since fungus spreads (and destroys any improvement on the squares it spreads to) eventually their city will very weak indeed.