Finding a delimiting character in a text file
The first way to deal with this issue is to examine what is the actual problem that you're attempting to solve.  Understand the problem fully before you solve it or you will end up with a mess.  There are two parts to why you might need this function...

1) You want to process the data.

To perform processing you are looking to extract blocks of numbers.  Knowing the delimiter is not relevant to your processing of the data.  You're looking for 1 or more numbers which are contiguous and anything that is not a number can be ignored until you hit another number block.  

That's your matrix processing taken care of without having to ever address any of your concerns or having a findDelimiter at all.

2) You want to reformat the file

If you want to output a formatted file with the same delimiter then your overall idea to identify a delimiter by building a frequency table and excluding certain values is on the right track.

To handle the issue of spaces, you can just set the [space] count to a maximum of 1 and if no other delimiters are present then then [space] will be the most frequent character.

There are some potential issues since you're dealing with arbitrary input.  You have no guarantee the delimiter will remain constant throughout the file; it wouldn't be unreasonable to see two matrix files concatenated for example.  

Equally you can avoid dealing with the very large datatypes if you limit your scanning to the first few kilobytes of a file.  This would also provide a usable result without the overhead of processing the whole file; though you could argue that it's premature optimisation I would consider it justified in this case as you are expecting very large files.  

Other potential issues...

This code assumes ASCII so far as I can tell.  There could be some "undefined behaviour" should someone give this code a file with Unicode content.

You spelled delimiter as delimeter - while this shouldn't be a big issue as most IDE's autocomplete, it's worth keeping an eye on as if another coder worked on your code and spelled it properly there could be confusion.  Many IDE's offer spellcheck and you should make sure yours is set up.

isNumeric will be an existing function.  Though you could eliminate the need for it entirely by setting the frequency counts for characters you want to ignore (like 0...9 and control characters) to a frequency of 0 before you process the frequency table.  This would also help remove or manage some of the 'magic numbers' in your code and make the intent clearer.

It's good practice to delay defining variables until you need them.  This can be useful should you come to refactor the code as compiler errors will point out when you attempt to modify a variable before it has been initialised.

I'd like to see c and f have meaningful names and for there to be a few more blank lines to illustrate the program flow blocks - the steps of the process become more obvious with the blank lines (as they are here... build a frequency table, remove the unwanted values, de-emphasise space, find the most common term and return it).  When the higher levels are clearly visible it makes refactoring easier.

unsigned char findDelimiter(FILE * fileToScan)
{
    rewind(fileToScan);

    int character;
    long long int frequencies[UCHAR_MAX] = { 0 };
    while ((character = fgetc(fileToScan)) != EOF) {
        frequencies[character]++;
    }

    const char IGNORECHARS[] = "0123456789\r\n";
    // todo: set the IGNORECHARS frequencies to 0 here
    // todo: set [space] to a maximum of 1 here

    long long int maxFrequency = 0;
    unsigned char delimiter = '\0';
    for (character = 0; character &lt; UCHAR_MAX; character++) {
        if (frequencies[character] &gt; maxFrequency) {
            maxFrequency = frequencies[character];
            delimiter = character;
        }
    }

    return delimiter;
}


With the code formatted this way it's easier to see how you could split the frequency analysis from the file reading should you want to do that later.

delimiter should be initialised with a reasonable value like ',' or be checked to throw an exception if a delimiter has not been found.