Howard is a highly disturbed individual and it would appear he planned to kidnap Michelle before the alien attack ever happened. There is also evidence that he kept her sedated for a period of time due to her nails having grown as evidenced by her nail-polish.
Howard wants a surrogate daughter and the alien invasion is incidental to his real motive.
What Does The Ending Of 10 Cloverfield Lane Really Mean?
He is immediately protective of her when Emmett touches her, tells her
she will become a good cook like Megan and even dresses her in his
daughter's clothes. This may be why he kidnapped Michelle in the first
place; we see in the opening that he drives up behind her - could he
have ran her off the road while racing home to his bunker so he could
have a surrogate daughter for after the end of the world? I'd say it's
very likely; that crash isn't just from an accidental knock.
The article above discusses this abusive relationship and the coiled insanity of Howard in great detail and is certainly worth the read.