I am going to be working from home in IL as a salaried employee, but my employer is based in California. Do I pay IL income taxes, or CA income taxes? And if I pay CA income taxes, anyone know a good online CA tax estimator? 
As an Illinois resident, you pay Illinois tax.
Whether your employer withholds the Illinois tax is another question.
Lady Chance does this.
She telecommutes from Ohio for an office in Virginia of a corporation based in California.
She pays Ohio state taxes.