Protograph-based Raptor-like low-density parity-check codes (PBRL codes) are a recently proposed family of easily encodable and decodable rate-compatible LDPC (RC-LDPC) codes. These codes have an excellent iterative decoding threshold and performance across all design rates. PBRL codes designed thus far, for both long and short block-lengths, have been based on optimizing the iterative decoding threshold of the protograph of the RC code family at various design rates. In this work, we propose a design method to obtain better quasi-cyclic (QC) RC-LDPC codes with PBRL structure for short block-lengths (of a few hundred bits). We achieve this by maximizing an upper bound on the minimum distance of any QC-LDPC code that can be obtained from the protograph of a PBRL ensemble. The obtained codes outperform the original PBRL codes at short block-lengths by significantly improving the error floor behavior at all design rates. Furthermore, we identify a reduction in complexity of the design procedure, facilitated by the general structure of a PBRL ensemble.