Your tax-exempt interest entry shouldn't have an effect on your income.
Try this:
Go to My Account.
Go to Tools.
Go to View Tax Summary.
Go to Preview my 1040.
Look at line 8b. Your tax-exempt interest should be there, but not reported as taxable.
Now, go back and erase the tax-exempt interest on the input screen. Repeat the above steps and line 8b should be zeroed out. Is your tax still higher?
There could be a couple of reasons for that, one being you are getting hit with Alternative Minimum Tax.
Is there anything on line 45? If there is, that's it.
Tax-exempt interest is used in a lot of calculations to phase you out of things.
Make sure you end up reporting the tax-exempt interest on your final return.