Yes, Berlanti & Co. initially really wanted Supergirl tied into the "Arrowverse" but Nina Tassler et al. over at CBS preferred it to be its own thing. There was some noiose made about maybe if it proved to be successful they might try to link them, but last I heard that wasn't going to happen.
And, really, how do you explain that Superman has been active for ~10 years (even to the extent of a photo of him winning a Pulitzer) but somehow nobody in Star(ling) City or Central City knows anything about him? Best to keep them separate.