It is charging me on my NY state tax for my entire income and not just the income from NY. Why?

NY prorates your tax liability based on your income. I am going to assume you are a nonresident or part year resident and looking at NY tax on federal income, line 38.  If you keep going to line 45, you will see a percentage calculated for NY. That percent of NY income is multiplied by the NY tax to create your liability. You have to keep going down to see a percentage of NY income is then multiplied  to get your final tax bill on line 50.

For example:

NY tax on your federal income is $8,000

But only 10% of your income was earned in NY

NY tax liability will be 10% of $8,000 or $800.