Yeah, you can do this.

1. Go get yourself an OMNY card (at CVS/Duane Reade/the NY Transit Museum/etc).
2. Go to https://omny.info/ and make an account.
3. Add your OMNY card to your wallet as a travel card.
4. Add your Wageworks card to your account as a payment method.
5. In your wallet on the website, select your OMNY card. Choose "Set up reload" > "Scheduled reload". You can choose to reload whatever amount you want either monthly or weekly, as well as the day of the month/week you want the reload to happen.
6. On the last page, select your Wageworks card as the payment method.

When I had Wageworks I had it set up to pull all of my pretax funds into my OMNY account a day or two after it landed in my Wageworks account. I spent like 6 months never having to think about running out of time or money, never needing to buy any passes or recharge anything. It was heaven. Then my employer switched to Voya and it's been nothing but trouble. :( Hoping I can work out the kinks to make it all automatic again....