Why is it hard to breathe naturally when meditating? For me it is rather hard to breathe naturally while doing Samatha meditation. It makes it harder to concentrate because I'm always controlling my breath.

Do you have any suggestion how to overcome this problem? 

Is this a normal problem for a beginner in Samatha meditation?
In the beginning one tends to control the breath out of habit. The moment we think about the breath we tend to take it over. Even going as far as trying to even it out, make it pleasant, make it smooth. 

Sticking with it long enough one can realise that the breath is not completely controllable or always pleasant. Realising this one can think that the meditation is not done right, as if the mediator is failing, however this is part of the practise. Seeing your habit of clinging, of trying to control and seeing that it doesn't work, you slowly and momentarily let it go.

So my suggestion is to simply sticking with it and you'll find yourself slowly letting the breath rise and fall, rather than trying to control.