What's going on here? Business income drastically reducing refund

So I file jointly. My partner has W2 income, I have a small amount of income recorded on schedule C. 

I'll use random numbers to try and explain what's going on:


After putting in my partner's W2 (say it's $60,000), the federal refund is $2,000.

 

When input put in my gross on schedule C (say it's $2,000) it drops the refund to $1,000.


I did not pay taxes throughout the year, so having to pay is expected, however, it seems my schedule C income is being taxed at around 50%. Does this makes sense?