One of the cheapest early defenses are mines. A good minefield can save your colony from an early strike Just remember to lay them at a distance greater than the range of any anticipated attacking units. Unless you're playing a short game, one of the first things you'll need is a second mining station to feed materials to your hungry engineers and constructors.
Every complex has a weak spot.
Use fighters to attack your enemy's force. If your can bombard your enemy's complex from the water, build a fleet. Ships are tougher and faster than land units. After they fire their shots, load the missile crawlers back into the transports and retreat to safety.