I received a 1099Misc from my employer for a bonus, TurboTax is is asking all kinds of questions I don't have answers to regarding Schedule Cs. I'm not self-employed.

 This is an easy way to enter Box 3 income.

1. Sign in to TurboTax Online, click Continue your return, then pick up where I left off (if you are using TurboTax CD/ Download, then just open your return on your computer).

1. Click on Federal Taxes at the top of the screen.
2. At the bottom of Your Income box pick the option in blue to help me add other income, then jump to full list;
3. Scroll down the page to the last section titled: Less common Income and click show more;
4. Select start or update next to the last topic titled Miscellaneous Income, 1099-A, 1099-C;
5. Scroll down to the last option titled Other reportable income and select start or edit;
6. When it asks, "Any other reportable income?" say yes then type in a description and the amount to report it on your tax return.

This will place it on line 21 of your Form 1040

But I received a 1099-MISC

Yes, box 3 of Form 1099-Misc.

Box 3 is Other Income.

It states "do not enter income reported on 1099-MISC"

Your employer made a mistake.  Employee bonuses are supposed to be reported on your W-2, not on a 1099-MISC.  So I would enter your 1099-MISC as follows:

Less Common Income > Miscellaneous Income > Other Income not already reported on a W-2 or 1099-MISC  > "Yes" to Did you receive any other wages? > continue past the household employee and sick pay screens > "Yes" again to Did you earn any other wages > then check "Employee compensation that was not reported on a W-2" > and proceed on.  Carefully follow the directions on each screen that follows.

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Ok thank you. It is ok to do this even though Turbo Tax says "do not enter income reported on 1099-MISC"?

Yes, assuming you did not already enter the 1099-MISC.  The TurboTax instruction is a bit confusing.

I should have said that another option is to ask your employer to void the 1099-MISC and issue a corrected W2.