What is the physical reason that a glass surface becomes hydrophobic by silanization? (e.g. is it due to increase in surface roughness due to the long chains which is created on the glass surface? or ...)
Water has many, rather strong intramolecular bonds called hydrogen bonds, which influences many of its properties, for example being fluid even at high temperatures.
Wheter some thing is hydrophilic/hydrophobic is influenced mostly by the availability of places where hydrogen bonds can happen, these are either 1. bonds between hydrogen and an element with high electronegativity (e.g. O; N) 2. an orbital already filled with 2 electrons.
Because water molecules are also polar, charged or polar particles are also more hydrophilic. (e.g. salts)
Hydrophobic substances simply lack those features.
A good example illuminating this is that even small alkanes are quite insoluble in water whereas starch, a large molecule with many hydroxy groups is still soluble.
Of course water "tries" to minimize its surface energy for example by forming spherical (least surface are) drops. If a surface has many possibilities for bonds on the other hand, water wets it.
A silanized surface has many long alkane chains, and therefore few possibilities to form bond, ergo it is quite hydrophobic. (In contrary to the normal glass, which has many atoms with (formal) charge.)