Another solution which makes use of a delayed rule:

In[1]:= L1 = {{x1, y1}, {x2, y2}, {x3, y3}, {x4, y4}, {xn, yn}};
L2 = L1 /. {x_, y_} :> {a x, y}

Out[2]= {{a x1, y1}, {a x2, y2}, {a x3, y3}, {a x4, y4}, {a xn, yn}}

.

In[1]:= L1 = {{x1, y1}, {x2, y2}, {x3, y3}, {x4, y4}, {xn, yn}};
L2 = Map[{a*First[#], Last[#]} &, L1]

Out[2]= {{a x1, y1}, {a x2, y2}, {a x3, y3}, {a x4, y4}, {a xn, yn}}


In[3]:= L2 = Map[{a, 1}*# &, L1]

Out[3]= {{a x1, y1}, {a x2, y2}, {a x3, y3}, {a x4, y4}, {a xn, yn}}


In[4]:= f[v_] := {a*First[v], Last[v]};
L2 = Map[f, L1]

Out[5]= {{a x1, y1}, {a x2, y2}, {a x3, y3}, {a x4, y4}, {a xn, yn}}


In[6]:= f[v_] := {a, 1}*v;
L2 = Map[f, L1]

Out[7]= {{a x1, y1}, {a x2, y2}, {a x3, y3}, {a x4, y4}, {a xn, yn}}


In[8]:= f[{x_, y_}] := {a*x, y};
L2 = Map[f, L1]

Out[9]= {{a x1, y1}, {a x2, y2}, {a x3, y3}, {a x4, y4}, {a xn, yn}}


In[10]:= f[{x_, y_}] := {a*x, y};
L2 = f /@ L1

Out[11]= {{a x1, y1}, {a x2, y2}, {a x3, y3}, {a x4, y4}, {a xn, yn}}


In[12]:= L2 = Transpose[{a*First[Transpose[L1]], Last[Transpose[L1]]}]

Out[12]= {{a x1, y1}, {a x2, y2}, {a x3, y3}, {a x4, y4}, {a xn, yn}}


In[13]:= t = Transpose[L1];
L2 = Transpose[{a*First[t], Last[t]}]

Out[14]= {{a x1, y1}, {a x2, y2}, {a x3, y3}, {a x4, y4}, {a xn, yn}}


In[15]:= L2 = L1;
For[i = 1, i <= Length[L1], i++, L2[[i, 1]] = a*L2[[i, 1]] ];
L2

Out[17]= {{a x1, y1}, {a x2, y2}, {a x3, y3}, {a x4, y4}, {a xn, yn}}

It seems like there should be a simple way to use the AffineTransform function to accomplish this.