Hi everyone.
I just tried clicker with my dog and she was very scared of the sound. I tried clicking and then throwing her a treat but that didn't work. Yes I was using the i-click.
Now she won't come near me!
Sadie is a mastiff/boxer mix about 3 years old. I got her from a shelter and she was very timid and shy at first. The shelter people told me they believe her owners just left her in their backyard all the time so the dog they had would have some company. When that dog died they returned Sadie to the shelter. She seems afraid whenever I raise my hand like to wave at someone also. She also has no idea how to play. In fact at first she would run from me when I would throw a ball or toy.
Sadie is doing better now and isn't near as timid as she was. She is very affectionate with me and will run and play some now.
I hope I haven't undone all I had accomplished with her in the last month. Maybe clicker training ISN'T for all dogs! 
Clicker training is for all dogs :o)
But some dogs do startle at the sound of the clicker. Luckily the clicker is not a magic box. It is a marker, it distinctive sound marks a specific behaviour that you would like to see repeated. Almost anything can be used as a marker, as long as it is something the dog do not hear all the time.
Suggestions:
try using a ball point retractable pen, it makes a very soft click.
try using a mouth click - most people that do this by clicking their tongue.
as long as you train in a way where she can see it, you could even use a little pen-flashlight - but it can be difficult to make sure the dog see the light.
Best of luck
Christina