Você pode tentar isso:
SELECT company_id
FROM tbl_company_tag_link
WHERE tag_id IN (1,2,3)
GROUP BY company_id
HAVING COUNT(DISTINCT tag_id ) = 3
SQL FIDDLE DEMO
SELECT company_id
FROM tbl_company_tag_link
WHERE tag_id IN (1,2,3)
GROUP BY company_id
HAVING COUNT(DISTINCT tag_id ) = 3
