I recently bought a DE0 FPGA board with GPIO headers.
The schematics shows that some of them are protected with BAT54S Schottky diodes. Does it mean that if I input 5v logic level they will be converted to 3.3V and protect the FPGA or do I need to step down the voltage by myself?
What is the easiest-safe way of converting 5v to 3.3v ?
Those diodes protect the pins from overvoltage, undervoltage, and electrostatic discharge. Basically, they prevent the voltage on the pin from crossing outside of the supply voltages, in this case above 3.3 or below 0.
If you want to feed in a 5v signal, put in a series resistor of maybe 100 to 1k ohms or so. The diode will clamp the voltage and the resistor will prevent too much current from being drawn from whatever is sourcing the signal. This only works for low speed signals. If you need something fast, then getting a dedicated level shifter chip is a better idea.
Those are clamp diodes. They prevent the voltage on the pin from going above Vcc+Vf or below GND-Vf. They do not perform level conversion, and they should not be used to do so since they usually can't take a lot of abuse.
The easiest way to perform level conversion is to use a IC such as TI's TXB01xx chips, but it is possible to use a MOSFET with some pullups for it.
Those diodes are more than likely for surge/ESD protection as oppose to "voltage level conversion" IF you were to connect 5V to one of these then yes they would be "clamped" via a diode to the 3v3 rail, but they would draw an increase in current from whatever is sourcing that pin
You asked
What is the easiest-safe way of converting 5v to 3.3v ?
This seems to imply that you are using the GPIOs as input only. If so, you can get away with a voltage divider on each input pin:
simulate this circuit – Schematic created using CircuitLab
Assuming the load is high-impedance (>1Mohm), these resistor values should work fine.
