You are confusing two completely separate things. Your self-employed income is reported on schedule C. You also report any ordinary and necessary expenses that you incurred in order to produce that income. Your taxable self-employment income is your gross income minus your business expenses. That is what you pay income tax and self-employment tax on.
then, your taxable business income flows from schedule C to the main form 1040 where it is combined with any other taxable income you might have, such as from a W-2 job, or investments, prizes, and other miscellaneous income. That creates your total taxable income. Then you list all of your personal deductions, credits, and dependents. You have the option of taking the standard deduction or the itemized deduction for certain personal expenses which reduces your total taxable income.
In other words, you most certainly should include all of your legitimate, ordinary and necessary business expenses on schedule C, even if you plan on taking the standard deduction as your personal deduction on form 1040.
