It is quite common to find that your replacement tube's Presta valve stem does not protrude far enough from the rim to attach a pump head or a CO2 spigot. If this happens on the trail, the consequences can be pretty severe. Here's a two-dollar solution that can be purchased at any bike shop. While there are many Presta Valve extensions available, the shorter Presta-to-Schrader adapter stabilizes (and can even extract) a shortie stem and allows you to fill your tires at gas stations in a pinch.
The valve stem is too short. There is no way to get a pump on this.
Use a Presta-to-Schrader adapter to extend it. This one came free with a Hutchinson aerosol tire sealer.
Most pumps and CO2 inflators can switch hit with Presta or Schrader valves. The adapter pulls the valve stem up through the rim hole to make a seal. Make sure you unscrew the Presta valve's seat before you attempt to inflate the tire. Then just leave the adapter on the wheel.