Protograph-based Raptor-like low-density parity-check codes (PBRL codes) are a family of easily encodable rate-compatible low-density parity-check (LDPC) codes. PBRL codes have an excellent performance across all design rates. Quasi-cyclic (QC) PBRL code families permit high-speed decoder implementations. 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 PBRL family at various design rates. This paper introduces a design method to obtain better QC PBRL code families at short block-lengths (of a few hundred bits) for low frame error rate (FER) requirements. We first select a protomatrix for the highest design rate. To add a new row to lower the rate, we keep all the previously obtained rows of the PBRL protomatrix fixed and select the new row that maximizes an upper bound on the minimum distance of any QC-LDPC code that can be obtained from the protomatrix. The new QC PBRL code families outperform the original PBRL codes at short block-lengths by providing a significantly better low-FER performance. The standard approach to computing the aforementioned upper bounds requires complexity that grows exponentially with the size of the protomatrix. However, we show that the structure of the PBRL protomatrix lets us obtain the upper bounds with complexity that grows only linearly with the size of the PBRL protomatrix. Using the complexity reduction results, we also establish an equivalence between the exhaustive search to design a new row for the PBRL protomatrix according to the new design method and an integer linear program.