How to creat Hrdrophobic ITO?

I'm not sure what the problem is, but consider that (CH3)3SiCl + H2O ->

(CH3)3Si-O-Si-(CH3)3 + 2 HCl. How dry was your solution? Is acid damaging to the ITO, which is present as a thin film on top of the glass? Also, what exactly did the glass look like after silanization? Was it at all cloudy or appear to have some sort of different coating on it (if you can see anything new at all, you deposited too much silane, which could effect the conductivity and the optical properties of the underlying layer of ITO).

Gonna have to disagree with Uncle Al - it'll take more far more than 60 seconds for any sort of complete coverage with (CH3)3SiCl. The smaller the molecule, the longer it takes to adsorb a monolayer (in my experience). But 5 hours should be enough, assuming you can keep things dry. Try dry refluxing too.

This silane is not a good choice for making very hydrophobic surfaces by the way, it will resist forming a monolayer. You really need a long alkyl chain on there to get the van der Waals stabilization necessary. Having only one Cl on the Si will prevent bulk polymerization, but increasing up to 3 Cl's will improve reactivity with the surface. The more Cl's, the more water-sensitive, and you will need very dry conditions, not just in your beaker but in your atmosphere. You can also try methoxy or ethoxy groups instead of Cl's, they are more water-stable.

In glass fibre coatings, it was normal to use vinyl silanes, applied in aqueous solution, to produce the keying agent on the glass surface. This, of course was subsequently dried in an oven. I don't think that hydrophobicity was a desired effect.