I am thinking you will need to add weights to let the chart know that it needs to share some space. Update your xml to have a weight attribute of 1 in the linear layout containing the checkboxes.
<?xml version="1.0" encoding="utf-8"?>
<LinearLayout xmlns:android="http://schemas.android.com/apk/res/android"
android:layout_width="match_parent"
android:layout_height="match_parent"
android:background="@color/background_color"
android:orientation="vertical" >
<!-- layout for chart -->
<LinearLayout
android:id="@+id/linearLayout_chart"
android:layout_width="match_parent"
android:layout_height="wrap_content"
android:orientation="vertical" >
</LinearLayout>
<!-- layout for checkboxes -->
<LinearLayout
android:layout_width="match_parent"
android:layout_height="wrap_content"
android:layout_weight="1"
android:orientation="horizontal" >
<CheckBox
android:id="@+id/checkBox1"
android:layout_width="0dp"
android:layout_height="wrap_content"
android:layout_weight="1"
android:checked="true"
android:text="checkBox1" />
<CheckBox
android:id="@+id/checkBox2"
android:layout_width="0dp"
android:layout_height="wrap_content"
android:layout_weight="1"
android:checked="true"
android:text="checkBox2" />
</LinearLayout>
</LinearLayout>