I don't disagree with the comments that seem hard to imagine you are still generating negative cash flow after holding a property for 11 years, that's tripled in value. When you factor in the principal payoff you may not have a negative cash flow. On the other hand, you have mentioned anything about expenses so your cash flow may be even more negative.
Your house has appreciated at almost 11% for the 11 years, that's less than the total stock market or S&P ~14%, but much better than foreign stocks ~6% or total bond ~2.5%. If you do sell you'll be in the 20% bracket for a least some of the gains so probably ~$110k this leaves you say $660K.
The problem is what do you do after you sell it. I know conventional wisdom on the board is to put into the stock market, which seems to me is replace one overvalued asset with another.
The only truly conservative investment is the 3-year Treasury at 2.56%, where it now earns more than 10 or 30-year bonds.
In truth, I need a lot more information before, I or frankly anybody could give you intelligent advice.
House location, rent, mortgage rate, maintenance and other costs, are you using a property manager comparable rents?
Plus information on the rest of your assets and current tax bracket.
If you currently have $500K in stocks, I'd say sell if you have $5 million, I'd say hold and between those two numbers I'd say it depends.