Air it out. Leave windows open during and after cleaning so that the chemicals don't linger in the air.
Buy "green" alternatives, like Seventh Generation and Mrs. Meyer's. Or look for products with these terms: biodegradable; plant-based; hypo-allergenic; formulated without dye or synthetic fragrance; non-flammable; does not contain chlorine, phosphate, petroleum, ammonia, acids, alkalized solvents, nitrates, or borates.
Make your own. Try:
A mix of baking soda and distilled white vinegar to scrub the toilet
Distilled white vinegar mixed with warm water to clean hardwood floors
Vegetable-based soap with a few drops of lavender essential oil to make an antiseptic cleaning spray
Do what you can. Using green cleaners even some of the time is better than never. To learn more, visit householdproducts.nlm.nih.gov