What is the down side of amortizing $3900 in business start up costs? If I claim it all now, I seem to get penalized. So will this be a good thing down the road?

The downside of amortizing is that you get a smaller deduction over 15 years.  I'm not sure what you mean by "penalized" if you take a deduction for the full $3,900 in startup costs. 

You can deduct up to $5,000 of startup costs as a current business expense.  The remainder is amortized over 180 months.  If you decide to amortize the startup costs, they will be a deduction against future income.

I guess by penalized I mean if I do the whole 3900, I seem to owe more federal tax. If I amortize say 50.00 I don't get hit as hard. I'm wondering when I start making money in the future, will the amortization hurt or help? Does that make sense?

I still don't understand why you would owe more tax if you take the $3900.  Amortization won't hurt -- it just means you take a smaller deduction over a longer time.