Molecular dynamics is often considered as a numerical experiment. The error bars on the results are therefore mandatory, but sometimes difficult to determine and computationally demanding. As a low-cost approach, we describe the application of the bootstrap (BS) method to the quantification of uncertainties pertaining to the time correlation functions. We chose the autocorrelation functions of velocity and interdiffusion current for a binary ionic mixture as a test bed, and we assessed the merit of the Darken approximation relating both of them. The intrinsic errors related to phase space sampling is investigated comparing the BS method with the reference method of replica. We also study how the BS method can assist in addressing the finite-size effects.