I don't think you can use bedtools intersect to intersect a BED file with a tab-delimited file that is not in BED format. Even though a BED file is essentially a tab-delimited file, it has a particular format. If you can convert your tab-file to BED format then maybe it will work.
Create a BED file out of your tab file, follow the steps below:
Add this line: #dummy header to a new empty file
Use awk or cut to extract from your tab-delimited file the fields corresponding to the BED file you already have. Redirect and append (>>) the output of this command to the file created above.
Use bedtools intersect on the BED files that you have now.
I don't think you can use bedtools intersect to intersect a BED file with a tab-delimited file that is not in BED format. Even though a BED file is essentially a tab-delimited file, it has a particular format. If you can convert your tab-file to BED format then maybe it will work.