How much can one trust them : The cufflinks output files (genes.fpkm_tracking, isoforms.fpkm_tracking) will contain confidence intervals for each of the FPKM estimates (under the headings FPKM_conf_lo and FPKM_conf_hi). Similarly, cuffdiff output also contains the FPKM estimates and confidence intervals used for differential expression testing. These intervals will give you an idea as to the extent of variability within each sample.
You could also do a pair-wise scatter plot of the FPKM values of each of your samples. That is, plot the FPKM values from sample 1 along the axis, and FPKM values from sample 2 on the y axis to look at how much variability is present in your data. The scatter should appear "elliptical", with the major axis along the y = x line if the variability between replicates is "low".
How "real" are these values : I didn't quite follow your question. FPKM values are estimates, and have errors associated with them due to many reasons. The confidence interval is an estimate of that error. Was that what you meant?