The fast version would be as follows:
if (inputEntry.charAt(i) == inputCharacter.charAt(0)) {
count++;
}
What happens is that you have declared inputCharacter as a String object, so obviously is not really a char or char[].
A better version for your little code snippet would be (since your little char will always be of single unit size):
int countz = StringUtils.countMatches(inputEntry, inputCharacter);
This allows for actual substring comparisons also. If you are really, really sure you want just one character inside your string, to be accounted for, then just use something like this:
int countz = StringUtils.countMatches(inputEntry, inputCharacter.charAt(0));