The line integration is being followed around the rectangle counter-clockwise, so the segment along which the magnetic field is B is parallel to the direction of integration, while the segment with ( B + dB ) is anti-parallel to the integration direction.
It's a matter of convention: one of the many applications of the right hand rule.
Point your thumb in the direction of the positive y-axis, and your fingers give the direction that is by convention positive.
This is shown by the arrowheads in the loop.
So B(x,t) is taken as positive, while B(x+dx,t) is taken as negative.