It is electrically safe to use a 6.3v ceramic cap on a 5v rail.
However, ceramic capacitors have a feature that the manufacturers are a bit coy about, the capacitance is voltage dependent, and you may not meet your required capacitance.
With most X7Rs, there's only a relatively small effect. However, if you choose a Y5U for instance, you can lose more than half of your rated capacitance by the time you get to the rated voltage. If the capacitor is stabilising the output of an LDO and needs to meet a minimum value, that can be important. You can lose another half if you operate at maximum temperature.
A further warning. Designations like X7R and Y5U only describe the tempco, not the voltco, and the effects depend on package size as well (not because of something spooky about package size, but because manufacturers use the cheapest ceramic that gets them to the target capacitance in any given package). As a rule of thumb, as the rated capacitance becomes more 'impressive' for the size, the voltco and tempco get worse. You must research ceramic capacitor choice down the the specific brand and package size if the minimum value is at all critical. The data is out there from reputable manufacturers. If you can't find it, don't use that brand, but you may have to dig deep on their sites, and even contact them for specifics.