Breathing rate monitoring using continuous wave (CW) radar has gained much attention due to its contact-less nature and privacy-friendly characteristic. In this work, using a single-channel CW radar, a breathing rate estimation method is proposed that deals with system nonlinearity of a single-channel CW radar and realizes a reliable breathing rate estimate by including confidence intervals. To this end, time-varying dominant Doppler frequency of radar signal, in the range of breathing rate, is extracted in time-frequency domain. It is shown through simulation and mathematical modeling that the average of the dominant Doppler frequencies over time provides an estimation of breathing rate. However, this frequency is affected by noise components and random body movements over time. To address this issue, the sum of these unwanted components is extracted in time-frequency domain, and from their surrogate versions, bootstrap resamples of the measured signal are obtained. Accordingly, a 95% confidence interval is calculated for breathing rate estimation using the bootstrap approach. The proposed method is validated in three different postures including lying down, sitting, and standing, with or without random body movements. The results show that using the proposed algorithm, estimation of breathing rate is feasible using single-channel CW radar. It is also shown that even in presence of random body movements, average of absolute error of estimation for all three postures is 1.88 breath per minute, which represents 66% improvement as compared to the Fourier transform-based approach.