Chromonic liquid crystals (CLCs) have drawn attention for applications to organic electronics and optical films as well as biological materials. Understanding the alignment mechanism of CLCs is important for those applications. Using a polarized transmission optical microscope, we observe the optical texture, dichroism, and birefringence of CLC films of sunset yellow (SSY) confined by polyamide (nylon) films that are rubbed with a brush. The films align with the stacks of SSY molecules oriented, surprisingly, perpendicular to the rubbing direction. We propose that this alignment is stabilized by molecular interaction between the stretched nylon chains and molecular grooves of the SSY stacks rather than elastic energy of the CLCs due to surface topography induced by the rubbing.