It can be good idea if it is fixed in bitcoin. When bitcoin price increases so is your salary. So there are chance that you can earn more if you receive it in btc. And when the price is low, you'll just hold it for a while and consider it as an investment.
If your company is directly using bitcoin in business, then I think that will not be a problem. And if not, then you can still have it in the contract that you will receive a fixed amount of bitcoin. But I think it is still a better idea to have your salary split into bitcoin and fiat. Fiat for immediate expenses and bitcoin for investment.